Multivalent protein kinetic property prediction method and related product

Abstract

The invention provides a multivalent protein kinetic property prediction method and a related product. According to a specific implementation mode of the method for predicting the kinetic properties of the multivalent protein, in the process of simulating the concentration change rate of a microstate where the multivalent protein is combined with an antigen on the surface of a cell membrane, the effective concentration of the combined antigen is adopted instead of the objective concentration of the combined antigen; and thus, the accuracy of predicting the kinetic properties of the multivalent protein combined to the surface of the cell membrane can be improved.

Description

TECHNICAL FIELD

[0001] Embodiments of the present disclosure relate to the field of bioinformatics, and in particular to a method for predicting the kinetic properties of multivalent proteins and related products. BACKGROUND

[0002] Multivalent interaction is a molecular mechanism of ligand and receptor. In nature, multivalent interaction widely exists in cell recognition and signal transmission processes. Due to many variable parameters, the application of this molecular mechanism to actual drug treatment still requires a lot of manpower and material resources for experimental screening.

[0003] Therefore, a theoretical model is needed to achieve rational design through algorithm simulation. At present, algorithm simulation is mainly carried out through thermodynamic models or kinetic models.

[0004] Traditional thermodynamic methods aggregate the binding free energy of each domain to derive the total affinity. However, many applications involving multivalent interactions occur far from equilibrium, requiring kinetic models to accurately capture these binding events.

[0005] Kinetic models usually decompose multivalent interactions into a state transition network between individual binding configurations, thereby determining the precise kinetics of multivalent binding and providing a comprehensive and dynamically accurate view of the entire system. As the number of valences increases, the number of unique binding configurations explodes, making kinetic simulation very time-consuming. Especially when dealing with high-valence binding and cell surface binding, the efficiency is low. In addition, existing models often ignore the complex conditions in the actual biological environment, lack consideration of cell membrane characteristics and spatial distribution, resulting in a gap between them and real biological processes. SUMMARY

[0006] Embodiments of the present disclosure provide a method, device, electronic equipment, storage medium and computer program product for predicting the kinetic properties of multivalent proteins.

[0007] In a first aspect, embodiments of the present disclosure provide a method for predicting the kinetic properties of multivalent proteins, the method comprising:

[0008] obtaining a three-dimensional spatial topology of a multivalent protein and binding kinetic parameters of each domain of the multivalent protein;

[0009] obtaining a state transition graph designed for the multivalent protein, wherein the state transition graph comprises a node set and a directed edge set, each node corresponds one-to-one to a microstate of the multivalent protein, and the multivalent protein transitions from a starting point microstate corresponding to a starting point of each directed edge to a terminal point microstate corresponding to a terminal point after binding a corresponding antigen at the corresponding domain, and transitions from the corresponding terminal point microstate to the corresponding starting point microstate after dissociating the corresponding antigen at the corresponding domain.

[0010] For a first binding directed edge in the state transition graph, an effective concentration of a first binding antigen corresponding to the first binding directed edge in a binding process corresponding to the first binding directed edge is determined as an objective concentration of the first binding antigen;

[0011] For a directed edge other than the first binding directed edge in the state transition graph, the following antigen effective concentration calculation operations are performed: obtaining an antigen density of an antigen corresponding to the directed edge; determining a binding distance of the antigen corresponding to the directed edge according to a diameter of the antigen corresponding to the directed edge; determining a volume ratio of a binding reaction volume of the antigen corresponding to the directed edge divided by a binding capture volume of a corresponding domain according to a three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; and determining an effective concentration of the antigen corresponding to the directed edge in a binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen.

[0012] Based on the effective concentrations of the antigens corresponding to the directed edges in the state transition graph, a concentration change rate equation set for each microstate corresponding to each node in the state transition graph is solved, wherein a concentration gain rate of an interaction between a domain and an antigen corresponding to a transition between a parent microstate of the microstate and the microstate in the concentration change rate equation for each microstate is calculated based on a binding kinetics parameter of the corresponding domain and an effective concentration of the corresponding antigen in a corresponding binding process.

[0013] In some optional embodiments, the determination of the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain according to the three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge comprises:

[0014] In response to determining that, at a starting point microstate corresponding to the directed edge, the domain corresponding to the directed edge has only one adjacent and bound antigen adjacent bound antigen domain, determining a binding capture hemisphere radius of the domain corresponding to the directed edge according to a linker topological length between the domain corresponding to the directed edge and the corresponding adjacent bound antigen domain, determining a binding capture volume of the corresponding domain according to the binding capture hemisphere radius corresponding to the directed edge, determining a binding reaction volume of the corresponding antigen according to the binding capture hemisphere radius corresponding to the directed edge and the binding distance of the corresponding antigen, and determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain as the volume ratio corresponding to the directed edge.

[0015] In response to determining the starting microstate of the directed edge, the domain corresponding to the directed edge has two adjacent domains that have bound antigens. Based on the topological length of the connector between the domain corresponding to the directed edge and the two adjacent domains that have bound antigens, and the binding distance of the directed edge to the antigen, the volume ratio of the binding reaction volume of the directed edge to the binding capture volume of the corresponding domain is determined.

[0016] In some alternative implementations, the binding kinetics parameters of the domains include binding rate and dissociation rate, and the concentration change rate equation for each microstate is:

[0017]

[0018] Among them, [S i ]、[S j ] and [S n [S] represents the i-th microstate S of the multivalent protein. i The j-th microstate S j and the nth microstate S n The concentration of P(S) j ) and C(S j S are respectively j Let be the set of parent microstates and the set of child microstates, where t is the time variable, and:

[0019] Multivalent proteins in S j The parent microstate S i binding antigen X i,j Convert to S j , For from S i binding antigen X i,j Convert to S j The binding rate of the corresponding structural domain during the process, [X i,j ] eff Antigen X i,j The multivalent protein from S i binding antigen X i,j Convert to S j Effective concentration during the process, For the multivalent protein from S i To S j Concentration gain rate;

[0020] The multivalent protein from S j Dissociation antigen X i,j Convert to S i , For the multivalent protein from S j Dissociation antigen X i,j Convert to S iThe dissociation rate of the corresponding structural domain during the process. For the multivalent protein from S j To S i The rate of concentration loss;

[0021] Because the multivalent protein in S i and S j Between the corresponding structural domains and antigen X i,j Interactions (binding or dissociation), For the multivalent protein in S i and S j The corresponding structural domains and antigen X i ,j The net rate of change in concentration of the interacting components;

[0022] Multivalent proteins in S j binding antigen X j,n Convert to S j The sub-microstate S n , For from S j binding antigen X j,n Convert to S n The binding rate of the corresponding structural domain during the process, [X j,n ] eff Antigen X j,n The multivalent protein from S j binding antigen X j,n Convert to S n Effective concentration during the process, For the multivalent protein from S j To S n Concentration gain rate;

[0023] The multivalent protein from S n Dissociation antigen X j,n Convert to S j , For from S n Dissociation antigen X j,n Convert to S j The dissociation rate of the corresponding structural domain during the process. For the multivalent protein from S n To S j The rate of concentration loss;

[0024] Because the multivalent protein in S j and S n Between the corresponding structural domains and antigen X j,n Interactions (binding or dissociation), For the multivalent protein in S j and Sn The corresponding structural domains and antigen X j,n The net rate of change in concentration of the interacting components;

[0025] For the multivalent protein in S j The rate of change of concentration.

[0026] In some optional embodiments, determining the effective concentration of the antigen corresponding to the directed edge based on the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density includes:

[0027] Substituting the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density into the following effective concentration calculation formula, the effective concentration of the antigen corresponding to the directed edge can be obtained:

[0028]

[0029] Among them, V S V represents the volume of the antigen binding reaction corresponding to the directed edge. tot The combined capture volume of the structural domain corresponding to this directed edge. Let δA be the antigen density corresponding to the directed edge, and N be the area per unit area. A δV is Avogadro's constant, and δV is the unit volume.

[0030] In some optional implementations, the method further includes:

[0031] For each node in the state transition diagram, a concentration-time sequence of the concentration of the multivalent protein in the corresponding microstate of the node is generated based on the concentration change rate equation obtained by solving the equation.

[0032] In some optional implementations, the method further includes:

[0033] Based on the concentration-time sequence of the multivalent protein at the corresponding microstate at this node, a concentration change curve of the multivalent protein at the corresponding microstate at this node is plotted.

[0034] In some optional embodiments, determining the binding distance of the directed edge corresponding to the antigen based on the diameter of the directed edge includes:

[0035] The binding distance of the directed edge corresponding to the antigen is determined by multiplying the diameter of the directed edge corresponding to the antigen by a preset ratio.

[0036] Secondly, embodiments of this disclosure provide a device for predicting the dynamic properties of multivalent proteins, the device comprising:

[0037] a first obtaining module, configured to obtain a three-dimensional spatial topology of a multivalent protein and binding kinetics parameters of each domain;

[0038] a second obtaining module, configured to obtain a state transition graph designed for the multivalent protein, wherein the state transition graph comprises a node set and a directed edge set, each node corresponds to a microstate of the multivalent protein, and the multivalent protein transitions from a starting point microstate corresponding to a starting point of each directed edge to an ending point microstate corresponding to an ending point of the directed edge after a corresponding domain binds to a corresponding antigen, and transitions from the ending point microstate to the starting point microstate after the corresponding domain dissociates from the corresponding antigen;

[0039] a first binding effective concentration determining module, configured to, for a first binding directed edge in the state transition graph, determine an effective concentration of a first binding antigen corresponding to the first binding directed edge in a binding process corresponding to the first binding directed edge as an objective concentration of the first binding antigen;

[0040] a second binding effective concentration determining module, configured to, for a directed edge other than the first binding directed edge in the state transition graph, perform the following antigen effective concentration calculation operation: obtaining an antigen density of an antigen corresponding to the directed edge; determining a binding distance of the antigen corresponding to the directed edge according to a diameter of the antigen; determining a volume ratio of a binding reaction volume of the antigen corresponding to the directed edge to a binding capture volume of a corresponding domain according to the three-dimensional topology of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; and determining an effective concentration of the antigen corresponding to the directed edge in a binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen.

[0041] a concentration change predicting module, configured to, based on the effective concentrations of the antigens corresponding to the directed edges in the state transition graph, solve a concentration change rate equation set for the microstates corresponding to the nodes in the state transition graph, wherein, for each microstate, a concentration gain rate of an interaction between a domain and an antigen corresponding to a transition between a parent microstate of the microstate and the microstate in the concentration change rate equation of the microstate is calculated based on a binding kinetics parameter of the corresponding domain and an effective concentration of the corresponding antigen in a corresponding binding process.

[0042] In some optional embodiments, the determination of the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge to the binding capture volume of the corresponding domain according to the three-dimensional topology of the multivalent protein and the binding distance of the antigen corresponding to the directed edge comprises:

[0043] In response to determining the starting microstate of the directed edge, the domain corresponding to the directed edge has only one adjacent bound antigen domain that has bound an antigen. Based on the topological length of the connector between the domain corresponding to the directed edge and the corresponding adjacent bound antigen domain, the binding capture hemisphere radius of the directed edge is determined. Based on the binding capture hemisphere radius of the directed edge, the binding capture volume of the corresponding domain is determined. Based on the binding capture hemisphere radius of the directed edge and the binding distance of the corresponding antigen, the binding reaction volume of the corresponding antigen is determined. The ratio of the binding reaction volume of the directed edge corresponding to the antigen to the binding capture volume of the corresponding domain is determined as the volume ratio of the directed edge.

[0044] In response to determining the starting microstate of the directed edge, the domain corresponding to the directed edge has two adjacent domains that have bound antigens. Based on the topological length of the connector between the domain corresponding to the directed edge and the two adjacent domains that have bound antigens, and the binding distance of the directed edge to the antigen, the volume ratio of the binding reaction volume of the directed edge to the binding capture volume of the corresponding domain is determined.

[0045] In some alternative implementations, the binding kinetics parameters of the domains include binding rate and dissociation rate, and the concentration change rate equation for each microstate is:

[0046]

[0047] Among them, [S i ]、[S j ] and [S n [S] represents the i-th microstate S of the multivalent protein. i The j-th microstate S j and the nth microstate S n The concentration of P(S) j ) and C(S j S are respectively j The set of parent microstates and the set of child microstates, where t is a time variable, and:

[0048] Multivalent proteins in S j The parent microstate S i binding antigen X i,j Convert to S j , For from S i binding antigen X i,j Convert to S j The binding rate of the corresponding structural domain during the process, [X i,j ] eff Antigen X i,j The multivalent protein from Si binding antigen X i,j Convert to S j Effective concentration during the process, For the multivalent protein from S i To S j Concentration gain rate;

[0049] The multivalent protein from S j Dissociation antigen X i,j Convert to S i , For the multivalent protein from S j Dissociation antigen X i,j Convert to S i The dissociation rate of the corresponding structural domain during the process. For the multivalent protein from S j To S i The rate of concentration loss;

[0050] Because the multivalent protein in S i and S j Between the corresponding structural domains and antigen X i,j Interactions (binding or dissociation), For the multivalent protein in S i and S j The corresponding structural domains and antigen X i ,j The net rate of change in concentration of the interacting components;

[0051] Multivalent proteins in S j binding antigen X j,n Convert to S j The sub-microstate S n , For from S j binding antigen X j,n Convert to S n The binding rate of the corresponding structural domain during the process, [X j,n ] eff Antigen X j,n The multivalent protein from S j binding antigen X j,n Convert to S n Effective concentration during the process, For the multivalent protein from S j To S n Concentration gain rate;

[0052] The multivalent protein from S n Dissociation antigen X j,n Convert to S j , is the concentration of the multivalent protein at S n dissociation of antigen X j,n transition to S j the dissociation rate of the corresponding domain in the process, is the concentration loss rate of the multivalent protein from S n to S j .

[0053] due to the interaction (binding or dissociation) of the corresponding domain of the multivalent protein with antigen X j between S n and S j,n , is the net rate of change of concentration of the corresponding domain of the multivalent protein interacting with antigen X j between S n and S j,n .

[0054] is the rate of change of concentration of the multivalent protein at S j .

[0055] In some optional embodiments, the effective concentration of the antigen corresponding to the directed edge is determined according to the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density, comprising:

[0056] substituting the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density into the following effective concentration calculation formula to obtain the effective concentration of the antigen corresponding to the directed edge:

[0057]

[0058] wherein V S is the binding reaction volume of the antigen corresponding to the directed edge, V tot is the binding capture volume of the domain corresponding to the directed edge, is the antigen density of the antigen corresponding to the directed edge, δA is the unit area, N A is the Avogadro constant, and δV is the unit volume.

[0059] In some optional embodiments, the device further comprises:

[0060] a concentration-time pair sequence generation module configured to generate, for a node in the state transition graph, a concentration-time pair sequence of the concentration of the multivalent protein at the microstate corresponding to the node over time according to the concentration change rate equation of the microstate corresponding to the node obtained by solving.

[0061] In some optional embodiments, the device further comprises:

[0062] The concentration change curve drawing module is configured to draw a concentration change curve of the concentration of the multivalent protein in the node corresponding microstate over time according to a concentration-time sequence of the concentration of the multivalent protein in the node corresponding microstate over time.

[0063] In some optional embodiments, the determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen corresponding to the directed edge comprises:

[0064] The product of the diameter of the antigen corresponding to the directed edge and a preset ratio is determined as the binding distance of the antigen corresponding to the directed edge.

[0065] In a third aspect, an embodiment of the present disclosure provides an electronic device, comprising: one or more processors; and a storage device having one or more programs stored thereon, wherein the one or more programs, when executed by the one or more processors, cause the one or more processors to implement the method described in any of the implementations of the first aspect.

[0066] In a fourth aspect, an embodiment of the present disclosure provides a computer-readable storage medium having a computer program stored thereon, wherein the computer program, when executed by one or more processors, implements the method described in any of the implementations of the first aspect.

[0067] In a fifth aspect, an embodiment of the present disclosure provides a computer program product comprising computer programs / instructions, wherein the computer programs / instructions, when executed by a processor, implement the method described in any of the implementations of the first aspect.

[0068] To solve the problems of high computational cost, long simulation time, and low accuracy due to not considering the characteristics and spatial distribution of the cell membrane in predicting the kinetic properties of the process of multivalent protein binding and cell membrane surface binding by using the existing application kinetics model, the multivalent protein kinetics property prediction method, device, electronic equipment, storage medium, and computer program product provided by the embodiments of the present disclosure, by obtaining the three-dimensional spatial topological structure of the multivalent protein and the binding kinetics parameters of each domain, then obtaining the state transition graph designed for the multivalent protein, wherein the state transition graph includes a node set and a directed edge set, each node corresponds to each microstate of the multivalent protein, and the multivalent protein converts from the starting point microstate corresponding to the starting point of each directed edge to the ending point microstate corresponding to the ending point after the corresponding domain binds to the corresponding antigen, and converts from the corresponding ending point microstate to the corresponding starting point microstate after the corresponding domain dissociates from the corresponding antigen, then for the first binding directed edge in the state transition graph, the effective concentration of the first binding antigen corresponding to the first binding directed edge in the binding process corresponding to the first binding directed edge is determined as the objective concentration of the first binding antigen, next for the directed edges other than the first binding directed edge in the state transition graph, the following antigen effective concentration calculation operation is performed: obtaining the antigen density of the antigen corresponding to the directed edge; determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen; determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge to the binding capture volume of the corresponding domain according to the three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; determining the effective concentration of the antigen corresponding to the directed edge in the binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen; and finally, based on the effective concentrations of the antigens corresponding to the directed edges in the state transition graph, the concentration rate equation set of each node corresponding to the microstate in the state transition graph is solved, wherein the concentration gain rate of the interaction between the corresponding domain and the antigen between the parent microstate and the microstate of each microstate in the concentration rate equation of the microstate is calculated based on the binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process. That is, by using the effective concentration of the bound antigen instead of the objective concentration of the bound antigen in the process of simulating the microstate concentration change rate of the multivalent protein binding to the antigen on the cell membrane surface, the accuracy of predicting the kinetic properties of the process of multivalent protein binding to the cell membrane surface can be improved. BRIEF DESCRIPTION OF DRAWINGS

[0069] Other features, objects, and advantages of the present disclosure will become more apparent from the following detailed description of non-limiting embodiments made with reference to the accompanying drawings. The drawings are for purposes of illustrating the specific embodiments only and are not to be construed as limiting the application. In the drawings:

[0070] Figure 1 is an exemplary system architecture diagram to which an embodiment of the present disclosure can be applied;

[0071] Figure 2A is a flowchart of an embodiment of a multivalent protein kinetic property prediction method according to the present disclosure;

[0072] Figure 2B is a flowchart of an embodiment of a decomposition according to step 204 of the present disclosure;

[0073] Figure 2C is a flowchart of an embodiment of a decomposition according to step 2043 of the present disclosure;

[0074] Figure 3A is a diagram of a space corresponding to a binding capture volume for which there is only one adjacent bound antigen domain, and a space in which a binding reaction volume for the corresponding antigen is located;

[0075] Figure 3B and Figure 3C is a diagram of a space corresponding to a binding capture volume for which there are two adjacent bound antigen domains, and a space in which a binding reaction volume for the corresponding antigen is located;

[0076] Figure 4 is shown in the left, middle, and right diagrams in FIG. 1 1;

[0077] Figure 5 is a structural diagram of an embodiment of a multivalent protein kinetic property prediction device according to the present disclosure;

[0078] Figure 6 is a structural diagram of a computer system of an electronic device suitable for use to implement an embodiment of the present disclosure. DETAILED DESCRIPTION

[0079] The present disclosure will be further described by way of illustration with reference to the accompanying drawings and embodiments. It is to be understood that the specific embodiments described herein are merely illustrative of the present disclosure and are not to be taken in a limiting sense. It is further noted that, for the sake of brevity, the figures of the drawings are not to scale and that relative dimensions of components do not reflect the actual scale thereof.

[0080] It is to be understood that the embodiments and features of the present disclosure can be interchanged between embodiments and the specific embodiments can be combined without conflict. The present disclosure will be described in further detail with reference to the drawings and embodiments.

[0081] Figure 1An exemplary system architecture 100 is shown, in which embodiments of the multivalent protein dynamics property prediction method and related products of this disclosure can be applied.

[0082] like Figure 1 As shown, system architecture 100 may include terminal devices 101, 102, and 103, a network 104, and a server 105. Network 104 serves as the medium for providing communication links between terminal devices 101, 102, and 103 and server 105. Network 104 may include various connection types, such as wired or wireless communication links, or fiber optic cables, etc.

[0083] Users can use terminal devices 101, 102, and 103 to interact with server 105 via network 104 to receive or send messages, etc. Various communication client applications can be installed on terminal devices 101, 102, and 103, such as web browser applications, bioinformatics applications, and speech recognition applications.

[0084] Terminal devices 101, 102, and 103 can be either hardware or software. When terminal devices 101, 102, and 103 are hardware, they can be various electronic devices with displays, including but not limited to smartphones, tablets, laptops, and desktop computers. When terminal devices 101, 102, and 103 are software, they can be installed on the terminal devices listed above. They can be implemented as multiple software programs or software modules (e.g., to provide distributed services) or as a single software program or software module. No specific limitations are made here.

[0085] In some cases, the method for predicting the kinetic properties of multivalent proteins provided in this disclosure can be executed by terminal devices 101, 102, and 103, and correspondingly, the device for predicting the kinetic properties of multivalent proteins can be set in terminal devices 101, 102, and 103. In this case, the system architecture 100 may not include server 105.

[0086] In some cases, the method for predicting the kinetic properties of multivalent proteins provided in this disclosure can be jointly executed by terminal devices 101, 102, and 103 and server 105. For example, the step of "obtaining the three-dimensional spatial topology of the multivalent protein, the binding kinetic parameters of each domain, and the mechanical properties of each linker" can be executed by terminal devices 101, 102, and 103, and the step of "performing the following effective antigen concentration calculation operation for each directed edge in the state transition diagram" can be executed by server 105. This disclosure does not limit this. Correspondingly, the device for predicting the kinetic properties of multivalent proteins can also be respectively set in terminal devices 101, 102, and 103 and server 105.

[0087] In some cases, the multivalent protein kinetics property prediction method provided by the present disclosure can be executed by the server 105, and accordingly, the multivalent protein kinetics property prediction device can also be arranged in the server 105, in which case the system architecture 100 can not include the terminal devices 101, 102, and 103.

[0088] It should be noted that the server 105 can be hardware or software. When the server 105 is hardware, it can be implemented as a distributed server cluster composed of multiple servers, or as a single server. When the server 105 is software, it can be implemented as multiple software or software modules (such as software for providing protein design services), or as a single software or software module. No specific limitation is made herein.

[0089] It should be understood that Figure 1 The number of terminal devices, networks, and servers in the system architecture 100 is merely illustrative. Depending on the implementation needs, there can be any number of terminal devices, networks, and servers.

[0090] With reference to Figure 2A , a flowchart 200 of one embodiment of a multivalent protein kinetics property prediction method according to the present disclosure is shown, which includes the following steps:

[0091] Step 201, obtaining the three-dimensional spatial topology of the multivalent protein and the binding kinetics parameters of each domain.

[0092] In the present embodiment, the execution subject of the multivalent protein kinetics property prediction method (for example, the server shown in Figure 1 ) can obtain the three-dimensional spatial topology of the multivalent protein, the binding kinetics parameters of each domain, and the mechanical properties of each linker from other electronic devices (for example, the terminal device shown in Figure 1 ) that are network-connected to the above execution subject, locally or remotely.

[0093] It should be noted that here, the multivalent protein (Multivalent proteins) refers to a protein that can simultaneously bind to multiple ligands, molecules, or domains, usually through multiple binding sites. Multivalent proteins can include but are not limited to the following types:

[0094] 1. Multisubunit Proteins, such as hemoglobin, antibodies, etc.

[0095] 2. Multidomain Proteins, such as Fibronectin, transcription factors (such as p53).

[0096] 4. Scaffold Proteins, such as Insulin Receptor Substrate (IRS), Post-Synaptic Density Protein (PSD-95), etc.

[0097] 5. Multivalent Receptors, such as Toll-like Receptors (TLRs), recognizing Pathogen- Associated Molecular Patterns (PAMPs) after dimerization, G-protein coupled receptors (GPCRs), etc.

[0098] 6. Viral Envelope Proteins, such as HIV gp120, Influenza Hemagglutinin (HA), etc.

[0099] 7. Artificially designed multivalent proteins: i.e., multivalent molecules constructed through protein engineering or synthetic biology for enhanced function or therapeutic applications. For example, multivalent antibodies (such as bispecific antibodies), DNA nanostructure conjugated proteins, etc.

[0100] The spatial topology data of multivalent proteins can contain multi-level information, which can be usually obtained through experimental determination, computational prediction, or database integration. As an example, the following gives some classification and acquisition methods of spatial topology data of multivalent proteins:

[0101] I. Key data of spatial topology of multivalent proteins

[0102] 1. Spatial arrangement data of domains, including:

[0103] Distribution of binding sites: relative arrangement of ligand binding sites on different domains (such as the geometric arrangement of multiple ligand binding pockets in multivalent receptors).

[0104] Connection mode between domains: conformation of linkers / flexible linker peptides or rigid connection regions (such as tandem of repeat domains in fibrin).

[0105] 2. Geometric parameters of linkers (such as topological length, bending angle). The topological length of the linker directly determines the maximum spatial separation distance between the functional domains, which is the "boundary condition" of the topology. The topological length is the physical length when the linker is fully stretched (such as the number of amino acid residues × the extension length of each residue ≈ 0.36-0.4 nm / residue).

[0106] For example: a 10-residue glycine-serine linker has a topological length of about 3.6-4 nm, which limits the maximum distance between two domains.

[0107] II. Data sources

[0108] 1. Experimental methods: e.g. X-ray Crystallography, Cryo-EM, NMR, SAXS, Cross-linking MS,

[0109] 2. Computational predictions and modeling: e.g. Homology Modeling, Docking, MD Simulation, etc.

[0110] 3. Database resources:

[0111] (1) General structural databases, e.g.:

[0112] PDB (https: / / www.rcsb.org / ): experimentally resolved protein structures;

[0113] UniProt (https: / / www.uniprot.org / ): integrated structural, functional, and sequence information.

[0114] (2) Specialized multivalent protein databases, e.g.:

[0115] Protein Interfaces (PISA): analysis of protein interaction interfaces in PDB.

[0116] 3DComplex: classification of protein oligomer topologies.

[0117] CORUM: database of mammalian protein complexes.

[0118] III. Data acquisition process

[0119] 1. Experimental priority:

[0120] If the target protein has no known structure, it needs to be resolved experimentally (e.g. Cryo-EM). Experimental data is uploaded to PDB / EMDB and made publicly available.

[0121] 2. Computational supplementation:

[0122] If experiments are not feasible, use AlphaFold2 to predict monomer structures, and then study multivalent assembly through docking or MD simulation.

[0123] Integrate experimental data such as cross-linking mass spectrometry to optimize the model.

[0124] 3. Database search:

[0125] Query known structures by PDB ID or UniProt ID.

[0126] Use PISA analysis interface, or 3DComplex to query similar oligomers.

[0127] The binding kinetics parameters of each domain of the multivalent protein can include binding rate kon, dissociation rate koff, affinity KD, etc., which can be determined and recorded in advance in practice by experiments. Then, the corresponding binding kinetics parameters can be obtained from the recorded storage location of the binding kinetics parameters. For example, the following experimental methods can be used: surface plasmon resonance (SPR), microscale thermophoresis (MST), stopped-flow spectroscopy, fluorescence polarization / anisotropy (FP / FA), single molecule techniques (such as TIRF, optical tweezers), etc.

[0128] It can be understood that the binding kinetics parameters of each domain of the multivalent protein can also be obtained from some professional databases. For example:

[0129] Kinetic Data of Biomolecular Interaction (KDBI), which includes protein-ligand kinetics parameters, at the website: http: / / xin.cz3.nus.edu.sg / group / kdbi.asp.

[0130] Biochemical Reaction Kinetics Database (SABIO-RK), at the website: https: / / sabio.h-its.org / .

[0131] The mechanical property data of each linker of the multivalent protein is used to describe the mechanical properties of the connection between the domains of the multivalent protein. As an example, some specific examples and corresponding acquisition methods are given below:

[0132] The mechanical properties of the linker usually include the following parameters:

[0133] 1. Rigidity / Flexibility parameter, which can include, for example:

[0134] Persistence Length (Lp): describes the bending stiffness of the linker (unit: nm).

[0135] In practice, the mechanical properties can be obtained by including but not limited to the following experimental methods:

[0136] 1. Single-Molecule Force Spectroscopy (SMFS)

[0137] By directly stretching the linker with Atomic Force Microscopy (AFM) or Optical Tweezers, the force-extension curve (fitting WLC or Free-Joint Chain model, FJC) and the unzipping path can be measured.

[0138] Example: Study the mechanical stability of antibody Hinge region.

[0139] 2. Fluorescence Resonance Energy Transfer (FRET)

[0140] By the efficiency change of donor-acceptor fluorescence pair, the length dynamics of the linker can be inferred, and the distance distribution and conformation ensemble can be output.

[0141] 3. Small Angle X-ray / Neutron Scattering (SAXS / SANS)

[0142] By applying this method, the overall shape parameters of the linker in solution (such as Rg, Dmax) can be obtained.

[0143] Database: SASBDB (https: / / www.sasbdb.org / ).

[0144] 4. Nuclear Magnetic Resonance (NMR)

[0145] The applicable scenario of nuclear magnetic resonance can be the local dynamics of short linkers (ps-ns time scale), and through nuclear magnetic resonance, the relaxation time (T1 / T2), order parameter, etc. can be obtained.

[0146] It can be understood that the mechanical properties of the linker can also be obtained by querying the structure database.

[0147] For example, the following professional databases can be queried:

[0148] PDB (https: / / www.rcsb.org / ), Protein Data Bank in Europe-EMDB, MolMeDB (Molecular Mechanics Database, https: / / molmedb.upol.cz / ).

[0149] Step 202, obtaining a state transition diagram designed for the multivalent protein.

[0150] Here, the state transition diagram can be designed in advance for the multivalent protein according to the actual task requirements. Here, the state transition diagram is used to describe the conformational changes, binding / dissociation events or functional state transitions of the multivalent protein in different microstates.

[0151] The state transition diagram can include a node set and a directed edge set. Each node in the node set corresponds to each microstate of the multivalent protein. That is, one node is associated with one microstate of the multivalent protein. The multivalent protein is converted from the starting point microstate corresponding to the starting point of each directed edge to the ending point microstate corresponding to the ending point after the corresponding domain binds to the corresponding antigen, and is converted from the corresponding ending point microstate to the corresponding starting point microstate after the corresponding domain dissociates from the corresponding antigen. Therefore, each directed edge corresponds to a domain of the multivalent protein and an antigen, and the antigen is associated with an antigen density.

[0152] In practice, an automatic method or a manual design method can be used to generate the state transition diagram for the multivalent protein. As an example, some specific implementation modes are provided below:

[0153] I. Method of automatically generating a state transition diagram

[0154] 1. Clustering analysis based on molecular dynamics (MD) trajectory:

[0155] Specifically, the trajectory of the MD simulation can be clustered first (such as K-means, DBSCAN), and similar conformations are classified into the same state. Then, the transition frequency between states is counted by a transition matrix to automatically generate a network diagram. For example, the following tools can be used: MDAnalysis (Python library) to analyze the trajectory and clustering, and PyEMMA or MSMBuilder to build a Markov state model (MSM) and generate a state transition diagram. In this process, the following parameters need to be specified: reaction coordinates (such as RMSD, principal components PCs) and the number of clusters (which needs to be evaluated by the elbow rule or VAMP).

[0156] 2. Markov state model (MSM)

[0157] Specifically, the conformational space is discretized into states, and the transition probability is described by a Markov chain. For example, the following tools can be used: Deeptime (https: / / deeptime-ml.github.io / ) and WESTPA (weighted dynamics simulation) to output the state transition diagram (nodes = states, edges = transition probability / rate).

[0158] 3. Prediction based on graph neural network (GNN)

[0159] This method is suitable for predicting unknown transition paths when part of the states are known. For example, DeepDriveMD (combining AI and MD) can be used.

[0160] II. Steps of manually designing state transition graph

[0161] Manual design is needed when there is lack of sufficient simulation data or need to combine experimental hypothesis. The key procedure is as follows:

[0162] 1. Define state nodes (Nodes)

[0163] Specifically according to the following:

[0164] Structural features: such as whether the domain binds to the ligand (free state, single binding state, double binding state, etc.).

[0165] Kinetic data: conformations distinguished by experiments (such as FRET, SPR).

[0166] Energy landscape**: stable states corresponding to free energy minima.

[0167] For example, for antibody-antigen multivalent binding, the following states can be designed:

[0168] State 1: free antibody (unbound).

[0169] State 2: one Fab binds to the antigen.

[0170] State 3: two Fabs bind to the antigen (bivalent state).

[0171] 2. Determine transition paths (Edges)

[0172] The following parameters need to be specified:

[0173] Energy barrier Estimated by umbrella sampling or transition state theory.

[0174] Rate constant (k): transition statistics from experiments (such as stopped-flow spectroscopy) or MD simulations.

[0175] The path determination rules may include, for example: only allow reasonable physical transitions (such as binding events need to meet spatial proximity), label reconfiguration changes (such as hinge region bending) or chemical modifications (such as phosphorylation triggers transition).

[0176] 3. Visualization tools

[0177] For example, the following software can be used for visualization:

[0178] Cytoscape: complex network visualization (annotated rates, energies).

[0179] Graphviz: automatic layout of state diagrams.

[0180] PyMOL / VMD: binding structure diagram transitions.

[0181] In step 203, for the first binding directed edge in the state transition diagram, the effective concentration of the first binding antigen in the first binding process corresponding to the first binding directed edge is determined as the objective concentration of the first binding antigen.

[0182] Here, the starting point of the first binding directed edge corresponds to a microstate in which the multivalent protein is in a free state, i.e., not bound to any antigen. The end point of the first binding directed edge corresponds to a microstate in which the multivalent protein has bound an antigen at only one domain, i.e., for the multivalent protein, it is the transition from the free state to the microstate corresponding to the end point of the first binding directed edge after first binding an antigen. Here, the antigen corresponding to the first binding directed edge is the first binding antigen.

[0183] It can be understood that there can be at least one first binding directed edge in the state transition diagram.

[0184] Since there is no influence of other antigens on the first binding of the multivalent protein, the effective concentration of the first binding antigen in the first binding process can be the objective concentration of the first binding antigen.

[0185] Here, the objective concentration (i.e., absolute concentration, not a relative value) of the antigen needs to be combined with quantitative experimental techniques and standard reference objects, and the specific method depends on the antigen type (soluble / membrane-bound) and the sample source (cell lysate, serum, tissue, etc.). The objective concentration of the first binding antigen can be measured in advance by experimental techniques, and the specific measurement method is not the focus of the present disclosure, and will not be described here.

[0186] In step 204, for the directed edges other than the first binding directed edge in the state transition diagram, an antigen effective concentration calculation operation is performed.

[0187] Here, the antigen effective concentration calculation operation can include the following steps 2041 to 2044 as shown in Figure 2B

[0188] In step 2041, the antigen density of the antigen corresponding to the directed edge is obtained.

[0189] Here, the antigen density refers to the density of the homologous antigen on the cell surface.

[0190] ​In practice, the antigen density of the antigen corresponding to each directed edge can be determined in advance by various means and stored, and then the execution subject can obtain the antigen density of the antigen corresponding to each directed edge from the corresponding storage location. As an example, some specific methods for determining the antigen density of the antigen are given below:

[0191] 1. Experimental direct measurement: For example, the following experimental methods can be used: fluorescence microscopy, flow cytometry (Flow Cytometry), atomic force microscopy (AFM), etc.

[0192] 2. Computational simulation and modeling. For example, it can include:

[0193] Prediction based on known structure: If the antigen is arranged in order (such as viral capsid protein), the number of antigens per unit area can be calculated from the crystal or Cryo-EM structure. Specific tools can be, for example, the measure density plug-in of PyMOL or the Voxel tool of Chimera.

[0194] Random spatial model: Assuming that the antigens are randomly distributed, the collision probability is simulated by Poisson distribution (suitable for soluble antigens in solution).

[0195] 3. Query database and literature

[0196] For example, the expression amount of part of the membrane protein can be obtained by querying the cell surface proteomics database (CSPA, Cell Surface Protein Atlas: [Human Protein Atlas](https: / / www.proteinatlas.org / )).

[0197] For example, published data can be queried to retrieve the antigen density of a similar system (such as the density of HIV envelope protein on the virus particle is about 14-72 per virus particle).

[0198] Step 2042, determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen corresponding to the directed edge.

[0199] Here, assuming that the cell membrane where the antigen is located is a plane, the antigen can move on the cell membrane plane. Then, the distance between the unbound domain of the multivalent protein and the cell membrane plane of the cell where the antigen is located needs to be less than or equal to the binding distance of the antigen to be combined with the antigen. Here, various implementations can be used to determine the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen corresponding to the directed edge. That is, the free domain is limited in a thin layer with a height of the binding distance, so that the conformational entropy of the free domain can be greatly reduced, thereby enhancing the local antigen search efficiency.

[0200] Optionally, the binding distance of the directed edge corresponding to the antigen can be determined by multiplying the diameter of the directed edge corresponding to the antigen by a preset ratio. As an example, the preset ratio can be 5%.

[0201] Step 2043: Based on the three-dimensional topological structure of the multivalent protein and the binding distance of the directed edge to the antigen, determine the volume ratio of the binding reaction volume of the directed edge to the antigen divided by the binding capture volume of the corresponding domain.

[0202] Here, we assume that the multivalent protein starts from the microstate S at the origin of the directed edge. i The structural domain d corresponding to the directed edge i,j The antigen X corresponding to the directed edge is bound at this location. i,j Then transition to the terminal microstate S of the directed edge. j Here, we assume the microstate S at the starting point of the directed edge. i The set of domains of a multivalent protein that have bound to an antigen is D. bound The set of unbound antigen domains is D. unbound The structure domain d corresponding to the directed edge i,j Belongs to the set of unbonded structural domains D unbound .

[0203] Here, the domain d i,j The combined capture volume V tot D used to characterize multivalent proteins bound If all domains in the structure have already bound to the antigen, then if it is necessary to bind to domain d i,j The maximum volume of space in which any antigen may be bound and captured.

[0204] Specifically, this can be achieved by analyzing the domain d in the three-dimensional spatial topological data of multivalent proteins. i,j Based on the spatial arrangement data of the directed edge and the spatial arrangement data of each combined structural domain corresponding to the directed edge, determine the structural domain d corresponding to the directed edge. i,j The combined capture volume.

[0205] Here, we assume the cell membrane containing the antigen is planar, allowing the antigen to move along this plane. Understandably, the distance between the unbound domain of the multivalent protein and the cell membrane plane of the cell containing the antigen to be bound must be less than or equal to the binding distance of the antigen for the antigen to bind to the unbound domain of the multivalent protein, thus enabling a reaction between the antigen and the multivalent protein. The directed edge corresponds to the antigen binding reaction volume V. s The structural domain d used to characterize the directed edge i,j The combined capture volume V tot Inner and structural domain d i,j The distance to antigen X corresponding to the directed edgei,j The binding distance h i,j The volume inside.

[0206] Various implementation methods can be used to calculate the antigen X corresponding to the directed edge. i,j The combined reaction volume V s Divide by the corresponding structural domain d i,j The combined capture volume V tot The ratio is then used to determine the volume ratio corresponding to the directed edge.

[0207] In some alternative implementations, step 2043 may include, for example: Figure 2C The following steps 20431 to 20435 are shown:

[0208] Step 20431: In response to determining the microstate at the starting point corresponding to the directed edge, the structural domain corresponding to the directed edge has only one adjacent adjacent bound antigen structural domain that has bound antigen. Based on the topological length of the connector between the structural domain corresponding to the directed edge and the corresponding adjacent bound antigen structural domain, the radius of the binding capture hemisphere corresponding to the directed edge is determined.

[0209] Here, if a multivalent protein is in the microstate S at the starting point of the directed edge... i The structure domain d corresponding to the directed edge i,j The existence of only one adjacent bound antigen domain indicates that the domain d corresponding to the directed edge is equal to the existence of only one adjacent bound antigen domain. i,j binding antigen X i,j The reaction is one in which only one side is bound to the cell membrane surface; a "beaded model" can be considered, where multivalent proteins are in the microscopic state S starting from the directed edge. i The structural domain d corresponding to the directed edge i,j The antigen X corresponding to the directed edge is bound at this location. i,j Then transition to the terminal microstate S of the directed edge. j During the process, antigen X i,j Restricted to the structural domain d corresponding to the directed edge i,j Within a hemispherical space centered on the center of the adjacent bound antigen domains and with the topological length of the connector corresponding to the directed edge as its radius, the topological length of the connector between the domain corresponding to the directed edge and its corresponding adjacent bound antigen domains is determined as the radius R of the binding capture hemisphere corresponding to the directed edge. t Then, proceed to step 20432 for execution.

[0210] Step 20432: Determine the combined capture volume of the corresponding structural domain based on the radius of the combined capture hemisphere corresponding to the directed edge.

[0211] Here, the formula for calculating the volume of a hemisphere can be used to capture the radius R of the hemisphere corresponding to the directed edge. t Calculate the hemispherical volume for the radius, and then define the calculated hemispherical volume as the combined capture volume V of the structural domain corresponding to the directed edge. tot Then, proceed to step 20433 for execution.

[0212] Step 20433: Determine the binding reaction volume of the corresponding antigen based on the radius of the binding capture hemisphere corresponding to the directed edge and the binding distance of the corresponding antigen.

[0213] Assume the directed edge corresponds to antigen X i,j The binding distance is h i,j In the structure domain d of the directed edge i,j binding antigen X i,j During the process, the structure domain d of the directed edge i,j With antigen X i,j For a given cell membrane plane to bind to an antigen, the distance between its constituent cells must be less than or equal to the binding distance of that antigen. Therefore, the directed edge domain d... i,j With antigen X i,j The space in which the bonding reaction occurs is confined within the directed edge corresponding to the structural domain d. i,j The combined capture volume V tot Within a frustum of a cone located within a hemisphere, the lower surface of the frustum coincides with the base plane of the hemisphere, and the height between the upper and lower surfaces of the frustum is h. i,j Furthermore, the formula for calculating the radius of a frustum can be used, combined with the above-mentioned formula, to capture the radius R of the hemisphere. t With radius h i,j Calculate the volume of the frustum for the height of the frustum, and use the calculated volume of the frustum as the antigen X corresponding to the directed edge. i,j The combined reaction volume V s Then, proceed to step 20434 for execution.

[0214] Step 20434: The ratio of the binding reaction volume of the antigen corresponding to the directed edge to the binding capture volume of the corresponding domain is determined as the volume ratio corresponding to the directed edge.

[0215] In other words, the directed edge can be represented here as antigen X. i,j The combined reaction volume V s Divide by the corresponding structural domain d i,j The combined capture volume V tot ratio The volume ratio corresponding to the directed edge is determined. After step 20434, step 2043 is executed in one case, and step 2043 can be terminated for this directed edge.

[0216] For convenience of understanding, please refer to Figure 3A , Figure 3A The figure shows the schematic diagram of the corresponding hemispherical space of the binding capture volume of the binding domain with only one adjacent bound antigen domain, and the space where the binding reaction volume of the corresponding antigen is located.

[0217] As shown in Figure 3A , the center of domain d i,j is P1, the center of the only one adjacent bound antigen domain d' i,j of domain d i,j is P2, the linker topological length between domain d' i,j and domain d i,j is R t , the binding capture volume V i,j of domain d tot corresponds to the volume of the hemispherical HC2 with P2 as the center. The binding reaction volume V i,j of antigen X s corresponds to the frustum FC in hemispherical HC2, the bottom plane of the frustum FC is the same as the bottom plane of hemispherical HC2, and the height of the frustum FC is h i,j .

[0218] In step 20435, in response to determining that in the starting microstate corresponding to the directed edge, the domain corresponding to the directed edge has two adjacent bound antigen domains, according to the linker topological length between the domain corresponding to the directed edge and the two adjacent bound antigen domains and the binding distance of the antigen corresponding to the directed edge, the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain is determined.

[0219] If the multivalent protein is in the starting microstate S i corresponding to the directed edge, the domain d i,j corresponding to the directed edge has two adjacent bound antigen domains, indicating that the reaction of the domain d i,j corresponding to the directed edge binding antigen X i,j is a reaction in which both sides are bound to the cell membrane surface, and the "bead string model" can be considered, and according to the linker topological length L1 and L2 between the domain d i,j corresponding to the directed edge and the two adjacent bound antigen domains and the binding distance h i,j of the antigen X i,j corresponding to the directed edge, the volume ratio of the binding reaction volume V i,j of the antigen X s corresponding to the directed edge divided by the binding capture volume V i,j of the corresponding domain d tot is determined. As an example, a specific implementation is given below:

[0220] Suppose that two adjacent bound antigen domains are domain i,j and domain , respectively. The linker topology length between domain i,j and domain is L1, and the linker topology length between domain i,j and domain is L2. During the process that the multivalent protein converts from the starting microstate S i of the directed edge to the ending microstate S i,j of the directed edge after binding the antigen X i,j corresponding to the domain d j of the directed edge, the antigen X i,j is confined in the intersection of the first hemisphere with the center of domain and the radius of L1, and the second hemisphere with the center of domain and the radius of L2. Assuming that the antigens are uniformly distributed, the distance between the center of the first hemisphere and the center of the second hemisphere is l, and is a function of the distance l, denoted as ρ(l). Under the assumption that the antigens are uniformly distributed, the mean value of ρ(l) can be solved first, and <ρ(l)> is determined as the ratio of the binding reaction volume V i,j of the antigen X s corresponding to the directed edge to the binding capture volume V ij of the corresponding domain d tot . As an example, a formula for calculating <ρ(l)> is given below:

[0221]

[0222] In the above formula, it is assumed that the antigens are uniformly distributed in the circular plane with the center O between the center of the first hemisphere and the center of the second hemisphere as the center and (L1+L2) as the radius. By integrating ρ(l) over the distance l between the center of the first hemisphere and the center of the second hemisphere in the range of 0 to (L1+L2), and averaging the integral result in the circular plane with (L1+L2) as the radius, <ρ(l)> can be obtained, which is equivalent to obtaining

[0223] For easy understanding, please refer to Figure 3B and Figure 3C , Figure 3B and Figure 3Cis a schematic diagram of the space between the intersection of the two hemispheres corresponding to the binding capture volume of two adjacent bound antigen domains, and the space where the binding reaction volume corresponding to the antigen is located.

[0224] As shown in Figure 3B , the center of domain d i,j is P1, and the two adjacent bound antigen domains of domain d i,j are domain d and domain d . A first hemisphere HCL is formed with the center PL of domain d as the center of the circle and the linker topological length L1 as the radius, and a second hemisphere HCR is formed with the center PR of domain d as the center of the circle and the linker topological length L2 as the radius. The bottom planes of the first hemisphere HCL and the second hemisphere HCR are in the same plane. In Figure 3B , the distance between the centers of the first hemisphere HCL and the second hemisphere HCR is L1+L2, and at this time, there is no intersection part between the first hemisphere HCL and the second hemisphere HCR, the binding capture volume V tot of domain d i,j is 0, and the binding volume V s of the corresponding antigen is also 0. In Figure 3C , the distance between the centers of the first hemisphere HCL and the second hemisphere HCR is less than L1+L2, and the binding capture volume V tot of domain d i,j corresponds to the intersection part HCI between the first hemisphere HCL and the second hemisphere HCR, the bottom plane of the intersection part HCI is the same as the bottom plane of the first hemisphere HCL and the second hemisphere HCR, and the height of the intersection part HCI is h i,j .

[0225] In step 2044, the effective concentration of the antigen corresponding to the directed edge in the binding process corresponding to the directed edge is determined according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen.

[0226] In some optional embodiments, the binding kinetics parameters of the domains include the binding rate and the dissociation rate, and the concentration change rate equation for each microstate can be:

[0227]

[0228] The above formula is the concentration change rate equation for a multivalent protein in the jth microstate S j , wherein [S i ], [S j ] and [S n ] are the concentrations of the multivalent protein in the ith microstate Si The j-th microstate S j and the nth microstate S n The concentrations of i, j, and n are non-negative integers.

[0229] P(S j ) and C(S j S are respectively j Let be the set of parent microstates and the set of child microstates, where t is the time variable, and:

[0230] Multivalent proteins in S j The parent microstate S i binding antigen X i,j Convert to S j , For from S i binding antigen X i,j Convert to S j The binding rate of the corresponding structural domain during the process, [X i,j ] eff Antigen X i,j In multivalent proteins from S i binding antigen X i,j Convert to S j Effective concentration during the process, For multivalent proteins from S i To S j Concentration gain rate;

[0231] Multivalent proteins from S j Dissociation antigen X i,j Convert to S i , For multivalent proteins from S j Dissociation antigen X i,j Convert to S i The dissociation rate of the corresponding structural domain during the process. For multivalent proteins from S j To S i The rate of concentration loss;

[0232] Due to the presence of multivalent proteins in S i and S j Between the corresponding structural domains and antigen X i,j Interactions (binding or dissociation), For multivalent proteins in S i and S j The corresponding structural domains and antigen X i,j The net rate of change in concentration of the interacting components;

[0233] Multivalent proteins in S j binding antigen X j,nTransition to S j Submicrostate S n , Transition from S j Binding of antigen X j,n Transition to S n Rate of binding of the corresponding domain during the process, j,n ] eff Antigen X j,n Effective concentration of the multivalent protein during the transition from S j Binding of antigen X j,n Transition to S n , Concentration gain rate of the multivalent protein during the transition from S j to S n ;

[0234] Dissociation of antigen X n Transition from S j,n Transition to S j , Rate of dissociation of the corresponding domain during the transition from S n Dissociation of antigen X j,n Transition to S j , Concentration loss rate of the multivalent protein during the transition from S n to S j ;

[0235] Due to the interaction (binding or dissociation) of the corresponding domain of the multivalent protein with antigen X j between S n and S j,n , Net rate of change of concentration of the interaction of the corresponding domain of the multivalent protein with antigen X j between S n and S j,n ;

[0236] Rate of change of concentration of the multivalent protein at S j .

[0237] It can be appreciated that when a domain on the multivalent protein initially binds to an antigen on the cell surface, subsequent binding is enhanced due to the increased probability of encounter between the antigen and other domains on the multivalent protein. This results in an effective concentration of [X eff (e.g., [X i,j ] eff , [X j,n ] eff ) [X i,j ] eff , [X j,n ] effapparent increase in concentration of [X] eff defined as the concentration of a hypothetical antigen that diffuses freely that would produce an equivalent probability of encounter. For a primary binding antigen reaction, the effective concentration can be considered to be the objective concentration of antigen in the system. For a non-primary binding antigen reaction, the effective concentration can be derived from the probability of encounter [X] eff .

[0238] The probability that an unoccupied domain at position R in 3D space encounters a hypothetical antigen Y that diffuses freely can be given by the expected number of antigen molecules in that unit volume δV (= 13) and can be expressed by the following equation:

[0239]

[0240] where r i represents the spatial position of the hypothetical antigen, r' represents the position of the unoccupied domain, [Y] is the molar concentration of the hypothetical antigen Y, N A is Avogadro's number, and δV is the unit volume.

[0241] Thus, the probability that a domain encounters a hypothetical antigen within its accessible space is given by the following equation:

[0242]

[0243]

[0244] where f(r) is the spatial distribution probability density function (PDF) that describes the probability of finding a domain at r, and V is the volume accessible to the domain.

[0245] Since P meet Y is proportional to [Y], the effective concentration [X] eff can be defined as follows:

[0246] [X] eff = [X] eff , when P meet X = P meet Y

[0247] The above equation can also be expressed as follows:

[0248]

[0249] where P meet X is the probability that a domain encounters antigen X on the surface of a cell. Thus, Pmeet X It determines the effective concentration [X] eff The only variable.

[0250] To calculate P meet X It can search for the binding between domains on multivalent proteins and target antigen X on the cell surface, which can be divided into two consecutive steps:

[0251] (1) Unoccupied (i.e., unbound antigen) domains must be close enough to the cell membrane;

[0252] (2) Unoccupied (i.e. unbound antigen) domains must encounter antigens on the cell membrane.

[0253] Therefore, the probability of meeting P meet X This can be represented as the product of two probabilities, specifically as follows:

[0254]

[0255] Where P surf It is the probability that an unoccupied domain is located near the cell surface. It is the probability that a near-surface domain encounters an antigen on the cell surface.

[0256] To calculate P surf Multivalent proteins can be processed using a "beaded model," where the cell membrane is considered a plane, and antigens can move on the cell membrane plane.

[0257] When a domain of a multivalent protein binds to an antigen on the cell membrane, that domain has one and only one adjacent, already bound domain. This soon-to-be-bound domain (or the domain remaining at the free end) is confined within a hemispherical volume V centered on its adjacent bound domain. tot Inward movement (e.g.) Figure 3A The hemispherical HC2 shown. At this point, if the binding domain of the multivalent protein enters a small volume V near the cell surface... s When this happens, bonding occurs, and the small volume V s The height of the antigen can be no more than 5% of the diameter of its homologous antigen.

[0258] Accordingly, P surf It can be calculated using the following formula:

[0259]

[0260] When a domain of a multivalent protein binds to an antigen on the cell membrane, the domain has two adjacent and bound adjacent bound domains, the domain that is about to bind (or the free end remaining domain) is limited in the intersection part of the two hemispheres centered on its two adjacent bound domains, i.e. the accessible volume V tot is the intersection of two hemispheres (such as Figure 3C the intersection part of two hemispheres HCI) shown in the figure. In this case, the above formula is approximated to be reasonable.

[0261] In summary, P can be calculated by surf .

[0262] Similar to the way P meet Y is calculated above, the probability of an unoccupied domain in V s meeting an antigen is given by the following formula:

[0263]

[0264]

[0265] where f 2D (r) is the distribution PDF describing the probability of finding a domain in a 2D plane, A is the accessible area of the domain, is the density of the homologous antigen on the cell surface, with a physical dimension of [L -2 ], δA is the unit area (=1 2 ), is the probability of an unoccupied domain meeting an antigen at position r.

[0266] In combination with the above equation, P meet X (reflecting [X] eff ) can be calculated as:

[0267]

[0268] Therefore, [X] eff can be calculated by the following formula:

[0269]

[0270] where can be obtained, δA, N A , δV are constants, and only needs to be calculated to calculate [X]eff, which has a small amount of calculation and can improve the calculation speed.

[0271] Accordingly, step 2044 can be performed as follows: substituting the binding capture volume of the corresponding domain of the directed edge, the binding reaction volume of the antigen, and the antigen density into the following effective concentration calculation formula to obtain the effective concentration of the antigen corresponding to the directed edge:

[0272]

[0273] wherein V S is the binding reaction volume of the antigen corresponding to the directed edge, V tot is the binding capture volume of the corresponding domain of the directed edge, and is the antigen density of the antigen corresponding to the directed edge, δA is the unit area, N A is Avogadro's constant, and δV is the unit volume.

[0274] After step 203 and step 204, the effective concentration of the antigen corresponding to each directed edge in the binding process corresponding to the directed edge can be obtained. Then, go to step 205 for further execution.

[0275] Step 205: based on the effective concentration of the antigen corresponding to each directed edge in the state transition graph, solve the concentration rate equation for the microstate corresponding to each node in the state transition graph.

[0276] Here, the concentration gain rate of the interaction between the domain and the antigen corresponding to the transition between the parent microstate and the microstate of the microstate in the concentration rate equation for each microstate is calculated based on the binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process.

[0277] Since the effective concentration of the antigen corresponding to each directed edge in the corresponding binding process has been obtained in step 204, the effective concentration of the antigen corresponding to each directed edge in the corresponding binding process and the binding kinetics parameters of the corresponding domain can be substituted into the concentration rate equation for each microstate, and the concentration rate equation for the microstate corresponding to each node in the state transition graph can be obtained. Further, based on the concentration rate equation of each microstate, subsequent analysis tasks can be performed.

[0278] In some optional embodiments, the above method 200 can further include the following step 206:

[0279] Step 206: for the node in the state transition graph, generating a concentration-time pair sequence of the concentration of the multivalent protein in the microstate corresponding to the node over time according to the concentration rate equation of the microstate corresponding to the node obtained by solving.

[0280] Since the concentration rate equation of each node corresponding microstate has been solved in step 205, here, for each node in the state transition graph, part of the nodes or all nodes, according to the concentration rate equation of the node corresponding microstate solved, after setting the corresponding time variable value range, the concentration time pair sequence of the concentration of the multivalent protein in the node corresponding microstate with time can be generated. Wherein, each concentration time pair includes time and concentration in the corresponding microstate.

[0281] Further, the professional and technical personnel can determine whether the designed state transition graph is reasonable, or whether the kinetic parameter design of each domain of the multivalent protein is reasonable and the like from the generated concentration time pair sequence of each node corresponding microstate.

[0282] In some optional embodiments, the above method 200 can further include the following step 207:

[0283] Step 207, according to the concentration time pair sequence of the concentration of the multivalent protein in the node corresponding microstate with time, draw the concentration change curve of the concentration of the multivalent protein in the node corresponding microstate with time.

[0284] As an example, the concentration change curve can be drawn with time in the concentration change time pair sequence as the horizontal axis coordinate and the corresponding concentration as the vertical axis coordinate, and the above concentration change curve can be presented to facilitate the professional and technical personnel to intuitively understand the concentration change of each microstate.

[0285] The multivalent protein kinetics property prediction method provided by the above embodiments of the present disclosure comprises the following steps: obtaining a three-dimensional spatial topological structure of a multivalent protein and binding kinetics parameters of each domain of the multivalent protein; obtaining a state transition graph designed for the multivalent protein, wherein the state transition graph comprises a node set and a directed edge set, each node corresponds to a microstate of the multivalent protein, and the multivalent protein transitions from a starting point microstate corresponding to the starting point of each directed edge to an ending point microstate corresponding to the ending point after the corresponding domain binds to the corresponding antigen, and transitions from the corresponding ending point microstate to the corresponding starting point microstate after the corresponding domain dissociates from the corresponding antigen; then, for a first binding directed edge in the state transition graph, the effective concentration of the first binding antigen corresponding to the first binding directed edge in the binding process corresponding to the first binding directed edge is determined as the objective concentration of the first binding antigen; next, for other directed edges in the state transition graph except the first binding directed edge, the following antigen effective concentration calculation operation is performed: obtaining the antigen density of the antigen corresponding to the directed edge; determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen; determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge to the binding capture volume of the corresponding domain according to the three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; determining the effective concentration of the antigen corresponding to the directed edge in the binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen; finally, based on the effective concentrations of the antigens corresponding to the directed edges in the state transition graph, the concentration change rate equation set of the microstates corresponding to each node in the state transition graph is solved, wherein the concentration gain rate of the interaction between the corresponding domain and the antigen between the parent microstate and the microstate of each microstate in the concentration change rate equation of the microstate is calculated based on the binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process. That is, by using the effective concentration of the bound antigen instead of the objective concentration of the bound antigen in the process of simulating the microstate concentration change rate of the multivalent protein binding to the antigen on the cell membrane surface, the accuracy of the kinetic property prediction of the multivalent protein binding to the cell membrane surface can be improved.

[0286] In addition to the above kinetic property prediction of the multivalent protein binding to the cell membrane surface, the applicant also simulates the binding of the multivalent protein in the solution. The solution model here has at least two main differences from the models in references 【1】 and 【2】.

[0287] Firstly, the model is extended to multivalent proteins with valence higher than three by accurately calculating the PDF of the domain to be bound of the multivalent protein with two bound antigen domains.

[0288] To calculate this PDF, we first independently calculate the PDF of the binding site relative to each domain, obtaining f(r) and g(r). Please refer to [reference needed] for details. Figure 4 , Figure 4 The three figures, left and right, illustrate diagrams related to PDF(r), f(r), and g(r).

[0289] from Figure 4 It can be seen that the total PDF, i.e., PDF(r), can be given by the normalized encounter probabilities of the two functions f(r) and g(r), as shown in the following formula:

[0290] PDF(r) = a·f(r)·g(r)

[0291] Where 'a' is the normalization factor, to ensure ∫∫∫ V PDF(r)dV=1.

[0292] Secondly, a novel algorithm derived from mathematical transformations accelerates the most time-consuming part of the computation, namely the three-dimensional convolution of radial functions:

[0293] Let f′: and g′: These are two radial functions defined in three-dimensional Euclidean space. There exists a scalar-valued function f: and g: Make

[0294] f′=f(‖r‖), g′=g(‖r‖)

[0295] Where |r| represents a vector The Euclidean norm. The convolution f′*g′ is given by the following formula:

[0296]

[0297] Since both functions are radial, the convolution integral can be more easily expressed in spherical coordinates.

[0298] Let r = ||r||, R = ||R||, and let Let r represent the angle between r and R. Therefore, the squared distance between r and R is given by the law of cosines:

[0299]

[0300] Convolution then becomes:

[0301]

[0302] This can be simplified to:

[0303]

[0304] This expression can be further simplified by replacing x' with

[0305]

[0306] where the function h(R,r) is defined piecewise as:

[0307]

[0308] This strategy converts the three-dimensional convolution integral into two one-dimensional integrals and reduces the time complexity of the convolution calculation by one polynomial degree.

[0309] Further referring to Figure 5 , as an implementation of the method shown in the above figures, the disclosure provides an embodiment of a polyvalent protein kinetic property prediction device, which corresponds to the method embodiment shown in Figure 2A , and the device can be applied in various electronic devices.

[0310] As shown in Figure 5 ​As shown, the multivalent protein kinetics property prediction device 500 of the embodiment comprises a first acquisition module 501, a second acquisition module 502, a first binding effective concentration determination module 503, a second binding effective concentration determination module 504, and a concentration change prediction module 505. Specifically, the first acquisition module 501 is configured to acquire the three-dimensional spatial topological structure of the multivalent protein and the binding kinetics parameters of each domain; the second acquisition module 502 is configured to acquire a state transition graph designed for the multivalent protein, wherein the state transition graph comprises a node set and a directed edge set, each node corresponds to a microstate of the multivalent protein, and the multivalent protein converts from the starting point microstate corresponding to the starting point of each directed edge to the ending point microstate corresponding to the ending point of the directed edge after the corresponding domain binds to the corresponding antigen, and converts from the ending point microstate to the starting point microstate after the corresponding domain dissociates from the corresponding antigen; the first binding effective concentration determination module 503 is configured to, for the first binding directed edge in the state transition graph, determine the effective concentration of the first binding antigen corresponding to the first binding directed edge in the binding process corresponding to the first binding directed edge as the objective concentration of the first binding antigen; the second binding effective concentration determination module 504 is configured to, for the directed edge other than the first binding directed edge in the state transition graph, perform the following antigen effective concentration calculation operation: acquiring the antigen density of the antigen corresponding to the directed edge; determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen; determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge to the binding capture volume of the corresponding domain according to the three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; determining the effective concentration of the antigen corresponding to the directed edge in the binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen; and the concentration change prediction module 505 is configured to solve the concentration change rate equation set for each microstate corresponding to each node in the state transition graph based on the effective concentration of the antigen corresponding to each directed edge in the state transition graph, wherein the concentration gain rate of the interaction between the corresponding domain and the antigen between the parent microstate and the microstate of each microstate in the concentration change rate equation of each microstate is calculated based on the binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process.

[0311] In the embodiment, the specific processing of the first acquisition module 501, the second acquisition module 502, the first binding effective concentration determination module 503, the second binding effective concentration determination module 504, and the concentration change prediction module 505 of the multivalent protein kinetics property prediction device 500 and the technical effects brought by the specific processing can be respectively referred to Figure 2AThe relevant descriptions of steps 201, 202, 203, 204 and 205 in the corresponding embodiments will not be repeated here.

[0312] In some optional embodiments, the determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain according to the three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge can comprise:

[0313] In response to determining that, in the starting microstate corresponding to the directed edge, the domain corresponding to the directed edge has only one adjacent and antigen-bound adjacent antigen-bound domain, determining the binding capture hemisphere radius of the domain corresponding to the directed edge according to the linker topological length between the domain corresponding to the directed edge and the corresponding adjacent antigen-bound domain, determining the binding reaction volume of the antigen corresponding to the directed edge according to the binding capture hemisphere radius of the directed edge and the binding distance of the corresponding antigen, and determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain as the volume ratio corresponding to the directed edge;

[0314] In response to determining that, in the starting microstate corresponding to the directed edge, the domain corresponding to the directed edge has two adjacent and antigen-bound domains, determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain according to the linker topological length between the domain corresponding to the directed edge and the two adjacent antigen-bound domains and the binding distance of the antigen corresponding to the directed edge.

[0315] In some optional embodiments, the binding kinetics parameters of the domain can include the binding rate and the dissociation rate, and the concentration change rate equation for each microstate can be:

[0316]

[0317] wherein [S i ], [S j ] and [S n ] are the concentrations of the multivalent protein in the i-th microstate S i , the j-th microstate S j and the n-th microstate S n , P(S j ) and C(S j ) are the parent microstate set and the child microstate set of S j , respectively, and t is the time variable, wherein:

[0318] The parent microstate set of S j ​i binding antigen X i,j Convert to S j , For from S i binding antigen X i,j Convert to S j The binding rate of the corresponding structural domain during the process, [X i,j ] eff Antigen X i,j The multivalent protein from S i binding antigen X i,j Convert to S j Effective concentration during the process, For the multivalent protein from S i To S j Concentration gain rate;

[0319] The multivalent protein from S j Dissociation antigen X i,j Convert to S i , For the multivalent protein from S j Dissociation antigen X i,j Convert to S i The dissociation rate of the corresponding structural domain during the process. For the multivalent protein from S j To S i The rate of concentration loss;

[0320] Because the multivalent protein in S i and S j Between the corresponding structural domains and antigen X i,j Interactions (binding or dissociation), For the multivalent protein in S i and S j The corresponding structural domains and antigen X i ,j The net rate of change in concentration of the interacting components;

[0321] Multivalent proteins in S j binding antigen X j,n Convert to S j The sub-microstate S n , For from S j binding antigen X j,n Convert to S n The binding rate of the corresponding structural domain during the process, [X j,n ] eff Antigen X j,n The multivalent protein from S j binding antigen X j,nConvert to S n Effective concentration during the process, For the multivalent protein from S j To S n Concentration gain rate;

[0322] The multivalent protein from S n Dissociation antigen X j,n Convert to S j , For from S n Dissociation antigen X j,n Convert to S j The dissociation rate of the corresponding structural domain during the process. For the multivalent protein from S n To S j The rate of concentration loss;

[0323] Because the multivalent protein in S j and S n Between the corresponding structural domains and antigen X j,n Interactions (binding or dissociation), For the multivalent protein in S j and S n The corresponding structural domains and antigen X j,n The net rate of change in concentration of the interacting components;

[0324] For the multivalent protein in S j The rate of change of concentration.

[0325] In some optional embodiments, determining the effective concentration of the antigen corresponding to the directed edge based on the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density may include:

[0326] Substituting the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density into the following effective concentration calculation formula, the effective concentration of the antigen corresponding to the directed edge can be obtained:

[0327]

[0328] Among them, V S V represents the volume of the antigen binding reaction corresponding to the directed edge. tot The combined capture volume of the structural domain corresponding to this directed edge. Let δA be the antigen density corresponding to the directed edge, and N be the area per unit area. A δV is Avogadro's constant, and δV is the unit volume.

[0329] In some optional embodiments, the apparatus 500 can further include:

[0330] a concentration time pair sequence generating module (not shown in the Figure 5 configured to, for a node in the state transition graph, generate a concentration time pair sequence of the concentration of the multivalent protein in the microstate corresponding to the node over time according to the solved concentration change rate equation of the microstate corresponding to the node.

[0331] In some optional embodiments, the apparatus 500 can further include:

[0332] a concentration change curve drawing module (not shown in the Figure 5 configured to draw a concentration change curve of the concentration of the multivalent protein in the microstate corresponding to the node over time according to the concentration time pair sequence of the concentration of the multivalent protein in the microstate corresponding to the node over time.

[0333] In some optional embodiments, the determining the binding distance of the antigen corresponding to the directed edge according to the diameter of the antigen corresponding to the directed edge can include:

[0334] multiplying the diameter of the antigen corresponding to the directed edge by a preset ratio to determine the binding distance of the antigen corresponding to the directed edge.

[0335] It should be noted that the implementation details and technical effects of each module and unit in the multivalent protein kinetics property prediction apparatus provided by the embodiments of the present disclosure can refer to the descriptions of other embodiments of the present disclosure, which will not be repeated here.

[0336] Reference is made below to Figure 6 which shows a structural schematic diagram of a computer system 600 suitable for implementing an electronic device of the present disclosure. Figure 6 The computer system 600 shown is merely an example and should not impose any limitation on the functions and use range of the embodiments of the present disclosure.

[0337] As shown in Figure 6 , the computer system 600 can include a processing device (such as a central processor, a graphics processor, etc.) 601, which can perform various appropriate actions and processes according to programs stored in a read-only memory (ROM) 602 or programs loaded from a storage device 608 into a random access memory (RAM) 603. In the RAM 603, various programs and data required for the operation of the computer system 600 are also stored. The processing device 601, the ROM 602, and the RAM 603 are connected to each other through a bus 604. An input / output (I / O) interface 605 is also connected to the bus 604.

[0338] Generally, the following devices can be connected to the I / O interface 605: input device(s) 606 including, for example, a touch screen, a touch pad, a keyboard, a mouse, a camera, a microphone, and the like; output device(s) 607 including, for example, a liquid crystal display (LCD), a speaker, a vibrator, and the like; storage device(s) 608 including, for example, a magnetic tape, a hard disk, and the like; and communication device(s) 609. The communication device(s) 609 can allow the computer system 600 to communicate wirelessly or wired with other devices to exchange data. Although Figure 6 The computer system 600 is shown with various devices, but it is understood that not all of the devices shown are required to implement or be present. More or less devices can alternatively be implemented or present.

[0339] In particular, the processes described above with reference to the flowcharts can be implemented as a computer software program according to embodiments of the present disclosure. For example, embodiments of the present disclosure include a computer program product comprising a computer program carried on a computer readable medium, the computer program containing program code for executing the methods illustrated by the flowcharts. In such embodiments, the computer program can be downloaded and installed from a network via the communication device 609, or installed from the storage device 608, or installed from the ROM 602. When the computer program is executed by the processing device 601, the above-mentioned functions defined in the methods of embodiments of the present disclosure are performed.

[0340] It should be noted that the computer-readable medium in the present disclosure can be a computer-readable signal medium or a computer-readable storage medium or any combination of the two. The computer-readable storage medium may, for example, but is not limited to, an electronic, magnetic, optical, electromagnetic, infrared, or semiconductor system, device or apparatus, or any combination of the above. More specific examples of the computer-readable storage medium can include, but are not limited to, an electrical connection having one or more wires, a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), an optical fiber, a portable compact disk read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the above. In the present disclosure, the computer-readable storage medium can be any tangible medium containing or storing a program that can be used by or in conjunction with an instruction execution system, device or apparatus. In the present disclosure, the computer-readable signal medium can include a data signal carried in a baseband or as a part of a carrier wave, which carries computer-readable program code. Such a propagated data signal can take many forms, including but not limited to an electromagnetic signal, an optical signal, or any suitable combination of the above. The computer-readable signal medium can also be any computer-readable medium other than the computer-readable storage medium, which can send, propagate or transmit a program for use by or in conjunction with an instruction execution system, device or apparatus. The program code contained in the computer-readable medium can be transmitted by any suitable medium, including but not limited to a wire, a cable, a RF (radio frequency) or the like, or any suitable combination of the above.

[0341] The computer-readable medium described above can be contained in the electronic device described above; or can exist separately and not be assembled into the electronic device.

[0342] The computer-readable medium described above carries one or more programs, which, when executed by the electronic device, cause the electronic device to implement the method for predicting the kinetic properties of polyvalent proteins as shown in the embodiments and optional implementation modes thereof. Figure 2A The method for predicting the kinetic properties of polyvalent proteins as shown in the embodiments and optional implementation modes thereof.

[0343] Computer program code for carrying out operations of the present disclosure can be written in any combination of one or more programming languages, including an object oriented programming language such as Java, Smalltalk, C++ or the like, and conventional procedural programming languages, such as the "C" programming language or similar programming languages. The program code can execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, partly on the user's computer and partly on a remote computer or entirely on the remote computer or server. In the latter scenario, the remote computer can be connected to the user's computer through any type of network, including a local area network (LAN) or a wide area network (WAN), or the connection can be made to an external computer (for example, through the Internet using an Internet Service Provider).

[0344] The flow diagrams and the block diagrams in the drawings are illustrations of architectures, functionalities, and operations of possible implementations of systems, methods, and computer program products according to various embodiments of the present disclosure. In this regard, each block in the flow diagrams or block diagrams can represent a module, a segment, or a portion of code, which comprises one or more executable instructions for implementing the specified logical function(s). It should also be noted that in some alternative implementations, the functions noted in the blocks can occur out of the order noted in the figures. For example, two blocks shown in succession may, in fact, be executed substantially concurrently or the blocks may

[0345] The units or modules described in the embodiments of the present disclosure can be implemented by software, or by hardware. In some cases, the name of the unit or module does not constitute a limitation on the unit itself. For example, a first obtaining module can also be described as a module that obtains the three-dimensional spatial topological structure of the polyvalent protein and the binding kinetics parameter of each domain.

[0346] The above description is merely that of preferred embodiments of the present disclosure and of the principles thereof. Those skilled in the art should understand that the scope of the disclosure is not limited to the specific combinations of technical features described above, and should also encompass other technical solutions formed by any combination of the above technical features or equivalent features, without departing from the above disclosed concept. For example, the above technical features can be replaced with other technical features disclosed in the present disclosure (but not limited to) having similar functions to form technical solutions.

[0347] [Reference 1] Errington, W. J.; Bruncsics, B.; Sarkar, C. A. Mechanisms of noncanonical binding dynamics in multivalent protein-protein interactions. Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 25659-25667.

[0348] [Reference 2] Bruncsics, B.; Errington, W. J.; Sarkar, C. A. MVsim is a toolset for quantifying and designing multivalent interactions. Nat. Commun. 2022, 13, 5029.

Claims

1. A method for predicting kinetic properties of a multivalent protein, comprising: obtaining a three-dimensional spatial topology of the multivalent protein and binding kinetics parameters of each domain; obtaining a state transition graph designed for the multivalent protein, wherein the state transition graph comprises a set of nodes and a set of directed edges, each node corresponds to a microstate of the multivalent protein, and the microstate at the start point of each directed edge transitions to the microstate at the end point after the corresponding domain binds to the corresponding antigen and transitions to the microstate at the start point after the corresponding domain dissociates from the corresponding antigen; for a first binding directed edge in the state transition graph, determining an effective concentration of the first binding antigen corresponding to the first binding directed edge in a binding process corresponding to the first binding directed edge as an objective concentration of the first binding antigen; for a directed edge other than the first binding directed edge in the state transition graph, performing the following antigen effective concentration calculation operation: obtaining an antigen density of the antigen corresponding to the directed edge; determining a binding distance of the antigen corresponding to the directed edge according to a diameter of the antigen; determining a volume ratio of a binding reaction volume of the antigen corresponding to the directed edge divided by a binding capture volume of the corresponding domain according to the three-dimensional topology of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; and determining an effective concentration of the antigen corresponding to the directed edge in a binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen; solving a set of concentration change rate equations for each microstate corresponding to each node in the state transition graph based on the effective concentrations of the antigens corresponding to each directed edge in the state transition graph, wherein a concentration gain rate of an interaction between a domain and an antigen corresponding to a transition between a parent microstate and a microstate in a concentration change rate equation for each microstate is calculated based on the binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process.

2. The method of claim 1, wherein, the determining of the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain according to the three-dimensional topology of the multivalent protein and the binding distance of the antigen corresponding to the directed edge comprises: in response to determining that there is only one adjacent bound antigen domain adjacent to the domain corresponding to the directed edge at the microstate corresponding to the start point of the directed edge, determining a binding capture hemisphere radius of the domain corresponding to the directed edge according to a linker topology length between the domain corresponding to the directed edge and the corresponding adjacent bound antigen domain, determining a binding capture volume of the corresponding domain according to the binding capture hemisphere radius corresponding to the directed edge, determining a binding reaction volume of the corresponding antigen according to the binding capture hemisphere radius corresponding to the directed edge and the binding distance of the corresponding antigen, and determining the volume ratio of the binding reaction volume of the antigen corresponding to the directed edge divided by the binding capture volume of the corresponding domain as the volume ratio corresponding to the directed edge; In response to determining that the starting microstate corresponding to the directed edge, two adjacent domains exist and have bound antigens corresponding to the directed edge, a volume ratio of a binding reaction volume of the antigen corresponding to the directed edge to a binding capture volume of the domain corresponding to the directed edge is determined according to a linker topological length between the domain corresponding to the directed edge and the two adjacent domains having bound antigens and a binding distance of the antigen corresponding to the directed edge.

3. The method of claim 1, wherein, The binding kinetics parameters of the domain include a binding rate and a dissociation rate, and a concentration change rate equation for each microstate is: wherein [S i ], [S j ] and [S n ] are the concentrations of the polyvalent protein in the i-th microstate S i , the j-th microstate S j and the n-th microstate S n , respectively, P(S j ) and C(S j ) are the parent and child microstate sets of S j , respectively, and t is the time variable, wherein: said multivalent protein in S j the parent microstate S i binding antigen X i,j to S j , the effective concentration of said multivalent protein in S i binding antigen X i,j to S j the rate of binding of the corresponding domains during the process of conversion of said multivalent protein from S i,j ] eff to S i,j the effective concentration of antigen X i in said multivalent protein during the process of conversion of said multivalent protein from S i,j binding antigen X j to S i the rate of gain in concentration of said multivalent protein from S j to S j ​ The multivalent protein dissociates antigen X from S j The multivalent protein dissociates antigen X from S i,j The multivalent protein dissociates antigen X from S i , The multivalent protein dissociates antigen X from S j The multivalent protein dissociates antigen X from S i,j The multivalent protein dissociates antigen X from S i The multivalent protein dissociates antigen X from S The multivalent protein dissociates antigen X from S j The multivalent protein dissociates antigen X from S i The multivalent protein dissociates antigen X from S due to the multivalent protein interacting (binding or dissociating) with antigen X i between S j and S i,j at the corresponding domains, is the net rate of change of concentration of the multivalent protein interacting with antigen X i between S j and S i,j at the corresponding domains. said multivalent protein in S j binding antigen X j,n to S j submicrostate S n , concentration of said multivalent protein in S j binding antigen X j,n to S n corresponding to the rate of binding of the domains during the process of conversion of said multivalent protein from S j,n ] eff concentration of antigen X j,n in said multivalent protein during the process of conversion of said multivalent protein from S j binding antigen X j,n to S n , concentration gain rate of said multivalent protein from S j to S n ; The multivalent protein dissociates from S n Dissociates antigen X j,n Converts to S j , The multivalent protein dissociates from S n Dissociates antigen X j,n Converts to S j The off rate of the corresponding domain during the process, The multivalent protein dissociates from S n to S j The concentration loss rate; Because the multivalent protein in S j and S n Between the corresponding structural domains and antigen X j,n Interactions (binding or dissociation), For the multivalent protein in S j and S n The corresponding structural domains and antigen X j,n The net rate of change in concentration of the interacting components; The multivalent protein is administered at a concentration that is sufficient to induce an immune response in the subject. j rate of change in concentration of the multivalent protein.

4. The method of claim 3, wherein, The effective concentration of the antigen corresponding to the directed edge is determined according to the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density, which includes: The effective concentration of the antigen corresponding to the directed edge is determined according to the binding capture volume of the domain corresponding to the directed edge, the binding reaction volume of the antigen, and the antigen density, which includes: where V S is the binding reaction volume of the antigen corresponding to the directed edge, V tot is the binding capture volume of the domain corresponding to the directed edge, is the antigen density of the antigen corresponding to the directed edge, δA is the unit area, N A is the Avogadro constant, and δV is the unit volume.

5. The method of claim 1, wherein, The method further includes: For a node in the state transition graph, a concentration time pair sequence of the concentration of the multivalent protein in the microstate corresponding to the node changing over time is generated according to the concentration change rate equation of the microstate corresponding to the node obtained by solving.

6. The method of claim 5, wherein, The method further includes: A concentration change curve of the concentration of the multivalent protein in the microstate corresponding to the node changing over time is plotted according to the concentration time pair sequence of the concentration of the multivalent protein in the microstate corresponding to the node changing over time. Preferably, the binding distance of the antigen corresponding to the directed edge is determined according to the diameter of the antigen corresponding to the directed edge, which includes: The product of the diameter of the antigen corresponding to the directed edge and a preset ratio is determined as the binding distance of the antigen corresponding to the directed edge.

7. A multivalent protein kinetics property prediction device, wherein, It includes: A first acquisition module configured to acquire a three-dimensional spatial topological structure of a multivalent protein and binding kinetics parameters of each domain; A second acquisition module configured to acquire a state transition graph designed for the multivalent protein, wherein the state transition graph includes a node set and a directed edge set, each node corresponds to a microstate of the multivalent protein, and the multivalent protein transitions from a starting microstate corresponding to a starting point of each directed edge to an ending microstate corresponding to an ending point after a corresponding domain binds a corresponding antigen, and transitions from the ending microstate to the starting microstate after the corresponding domain dissociates the corresponding antigen; A first binding effective concentration determination module configured to, for a first binding directed edge in the state transition graph, determine an effective concentration of a first binding antigen corresponding to the first binding directed edge in a binding process corresponding to the first binding directed edge as an objective concentration of the first binding antigen. The other binding effective concentration determination module is configured to perform the following antigen effective concentration calculation operations for other directed edges in the state transition graph except the first binding directed edge: obtaining an antigen density of an antigen corresponding to the directed edge; determining a binding distance of the antigen corresponding to the directed edge according to a diameter of the antigen; determining a volume ratio of a binding reaction volume of the antigen corresponding to the directed edge divided by a binding capture volume of a corresponding domain according to a three-dimensional topological structure of the multivalent protein and the binding distance of the antigen corresponding to the directed edge; and determining an effective concentration of the antigen corresponding to the directed edge in a binding process corresponding to the directed edge according to the volume ratio corresponding to the directed edge and the antigen density of the corresponding antigen. The concentration change prediction module is configured to solve a concentration change rate equation set for each microstate in the state transition graph based on the effective concentrations of the antigens corresponding to the directed edges in the state transition graph, wherein a concentration gain rate of an interaction between a domain and an antigen corresponding to a transition between a parent microstate and the microstate in the concentration change rate equation for each microstate is calculated based on binding kinetics parameters of the corresponding domain and the effective concentration of the corresponding antigen in the corresponding binding process.

8. An electronic device, comprising: comprising: one or more processors; a memory device having stored thereon one or more programs, when the one or more programs are executed by the one or more processors, cause the one or more processors to carry out the method of any one of claims 1-6.

9. A computer readable storage medium, wherein, a computer program stored thereon, wherein the computer program is executed by one or more processors to implement the method of any one of claims 1-6.

10. A computer program product, wherein, comprise computer programs / instructions that, when executed by a processor, implement the method of any one of claims 1-6.

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