Correction map calculation method, electronic device, storage medium and program product

Abstract

The invention discloses a calculation method of a correction map, electronic equipment, a storage medium and a program product, and relates to the technical field of molecular dynamics. The method comprises the following steps: performing dynamic simulation on target protein molecules to obtain a target dynamic model; the target dynamic model is composed of a plurality of square blocks; determining a target atom chain formed by connecting a target number of atoms in the target kinetic model; determining a target reference atom in each target atom chain, determining a target block where the target reference atom is located, and executing a correction map calculation task of the target atom chain based on a target calculation component of the target block; and in response to a completion instruction of the calculation task of each target atomic chain, obtaining a calculation result of the correction map of the target protein molecule. According to the scheme, calculation of the correction map of the protein structure can be achieved, and help is provided for ensuring that the force field can more accurately reproduce the potential energy surface derived by quantum and keeping the real protein conformation as time goes on.

Description

Technical Field

[0001] This invention relates to the field of molecular dynamics technology, and in particular to a method for calculating calibration spectra, an electronic device, a storage medium, and a program product. Background Technology

[0002] Molecular dynamics simulation (MD) is a method that uses computers to simulate the motion and evolution of molecular systems under certain conditions. It can be used to study the structure, properties, phase transitions, reactions, transport, and other phenomena of molecules, thereby revealing the microscopic mechanisms and macroscopic laws of matter.

[0003] The accuracy of molecular dynamics simulations depends on the accuracy of the force field, particularly how accurately it describes the protein backbone. Currently, traditional force fields struggle to replicate the accurate dihedral angles and conformational distributions of the main chain, especially in proteins. Inaccuracies in angles such as the ψ dihedral angle often lead to deviations from experimental protein structures. A key research focus in the field is how to calculate the calibration profile of protein structures to ensure that the force field can more accurately reproduce the quantum-derived potential energy surface, thus helping to maintain the true protein conformation over time. Summary of the Invention

[0004] This invention provides a method, electronic device, storage medium, and program product for calculating calibration maps of protein structures, which helps to ensure that the force field can more accurately reproduce the quantum-derived potential energy surface and maintain the true protein conformation over time.

[0005] According to one aspect of the present invention, a method for calculating a calibration spectrum is provided, the method comprising:

[0006] A dynamic simulation of the target protein molecule is performed to obtain a target dynamic model of the target protein molecule; wherein the target dynamic model is composed of multiple blocks, and each block contains atoms;

[0007] In the target dynamics model, a target atomic chain consisting of a target number of atoms is determined;

[0008] In each of the target atomic chains, a target reference atom is determined, and the target block in which the target reference atom is located is determined. Based on the target computing unit of the target block, the calibration spectrum calculation task of the target atomic chain is performed.

[0009] In response to the completion instructions of the computational tasks of each of the target atomic chains, the calculation results of the calibration map of the target protein molecule are obtained.

[0010] According to another aspect of the present invention, a calculation apparatus for correcting a spectrum is provided, the apparatus comprising:

[0011] The dynamics simulation module is used to perform dynamics simulations on the target protein molecule to obtain a target dynamics model of the target protein molecule; wherein, the target dynamics model is composed of multiple blocks, and each block contains atoms;

[0012] The target atomic chain determination module is used to determine the target atomic chain composed of a target number of atoms in the target dynamics model.

[0013] The calibration spectrum calculation task execution module is used to determine the target reference atom in each of the target atomic chains, and determine the target block where the target reference atom is located, and execute the calibration spectrum calculation task of the target atomic chain based on the target calculation unit of the target block;

[0014] The calculation result determination module is used to obtain the calculation result of the calibration spectrum of the target protein molecule in response to the completion instruction of the calculation task of each target atomic chain.

[0015] According to another aspect of the present invention, an electronic device is provided, the electronic device comprising:

[0016] At least one processor; and

[0017] A memory communicatively connected to the at least one processor; wherein,

[0018] The memory stores a computer program that can be executed by the at least one processor, which enables the at least one processor to perform the calibration spectrum calculation method according to any embodiment of the present invention.

[0019] According to another aspect of the present invention, a computer-readable storage medium is provided, the computer-readable storage medium storing computer instructions for causing a processor to execute and implement the method for calculating the calibration spectrum according to any embodiment of the present invention.

[0020] According to another aspect of the present invention, a computer program product is provided, comprising a computer program that, when executed by a processor, implements the method for calculating the calibration spectrum as described in any embodiment of the present invention.

[0021] The technical solution of this invention involves performing dynamic simulation on a target protein molecule to obtain a target dynamic model of the target protein molecule. The target dynamic model consists of multiple blocks, each containing atoms. A target atomic chain of a target number of atoms is determined within the target dynamic model. A target reference atom is determined in each target atomic chain, and the target block containing the target reference atom is identified. A target computing unit based on the target block executes a calibration spectrum calculation task for the target atomic chain. In response to the completion instruction of the calculation task for each target atomic chain, the calculation result of the calibration spectrum of the target protein molecule is obtained. This enables the calculation of the calibration spectrum of the protein structure, helping to ensure that the force field can more accurately reproduce the quantum-derived potential energy surface and maintain the true protein conformation over time.

[0022] It should be understood that the description in this section is not intended to identify key or essential features of the embodiments of the present invention, nor is it intended to limit the scope of the invention. Other features of the invention will become readily apparent from the following description. Attached Figure Description

[0023] To more clearly illustrate the technical solutions in the embodiments of the present invention, the accompanying drawings used in the description of the embodiments will be briefly introduced below. Obviously, the accompanying drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0024] Figure 1 This is a flowchart of a method for calculating a calibration spectrum according to Embodiment 1 of the present invention;

[0025] Figure 2 This is a schematic diagram of a cube for molecular dynamics simulation divided into multiple spaces, according to Embodiment 1 of the present invention.

[0026] Figure 3 This is a schematic diagram of the target atom chain provided in Embodiment 1 of the present invention;

[0027] Figure 4 This is a schematic diagram of the target reference atom in the target atom chain provided in Embodiment 1 of the present invention;

[0028] Figure 5 This is a flowchart of a method for calculating a calibration spectrum according to Embodiment 2 of the present invention;

[0029] Figure 6 This is a schematic diagram of the structure of a calibration spectrum calculation device provided in Embodiment 3 of the present invention;

[0030] Figure 7 This is a schematic diagram of the structure of an electronic device that implements the calculation method of the calibration spectrum in the embodiments of the present invention. Detailed Implementation

[0031] To enable those skilled in the art to better understand the present invention, the technical solutions of the present invention will be clearly and completely described below with reference to the accompanying drawings of the embodiments of the present invention. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort should fall within the scope of protection of the present invention.

[0032] It should be noted that the terms "first," "second," etc., in the specification, claims, and accompanying drawings of this invention are used to distinguish similar objects and are not necessarily used to describe a specific order or sequence. It should be understood that such data can be interchanged where appropriate so that the embodiments of the invention described herein can be implemented in orders other than those illustrated or described herein. Furthermore, the terms "comprising" and "having," and any variations thereof, are intended to cover non-exclusive inclusion; for example, a process, method, system, product, or apparatus that comprises a series of steps or units is not necessarily limited to those steps or units explicitly listed, but may include other steps or units not explicitly listed or inherent to such processes, methods, products, or apparatus.

[0033] Example 1

[0034] Figure 1 This is a flowchart of a calibration spectrum calculation method according to Embodiment 1 of the present invention. This embodiment is applicable to the calculation of calibration spectra for protein molecules. The method can be executed by a calibration spectrum calculation device, which can be implemented in hardware and / or software and can be configured in electronic devices such as computers, servers, or tablet computers. Figure 1 As shown, the method includes:

[0035] Step 110: Perform dynamic simulation on the target protein molecule to obtain the target dynamic model of the target protein molecule.

[0036] The target dynamics model consists of multiple blocks, and each block contains atoms.

[0037] In this embodiment, the target protein molecule can be an enzyme, structural protein, transport protein, immune system-related protein, storage protein, etc., and is not limited thereto in this embodiment.

[0038] Optionally, in this embodiment, when it is necessary to calculate the calibration spectrum of the target protein molecule, the target protein molecule can be subjected to dynamic simulation to obtain a dynamic model of the target protein molecule, which is referred to as the target dynamic model in this embodiment.

[0039] In this embodiment, the dynamics simulation of the target protein molecule can be performed in a cubic box with periodic boundaries. Each subspace (block) in the cubic box is mapped to a computing component according to its corresponding position in three-dimensional space. Specifically, these computing components are connected in a three-dimensional interconnection manner to form a scientific computing device for molecular dynamics simulation.

[0040] Each cube can store several atoms, some of which are bonded together. Calculating the interatomic forces requires data exchange between cubes. For each cube, a smaller interaction range with its surroundings results in higher data transfer efficiency, corresponding to fewer computational components transmitting data.

[0041] For example, Figure 2 This is a schematic diagram of a cube for molecular dynamics simulation divided into multiple spaces according to Embodiment 1 of the present invention, wherein a small cube represents a subspace, and each cube may contain multiple atoms. In this embodiment, the number of atoms in each cube is not limited.

[0042] Step 120: Determine the target atomic chain consisting of the target number of atoms in the target dynamics model.

[0043] The number of targets can be an odd number such as 3, 5 or 7, and this embodiment does not limit it.

[0044] Optionally, in this embodiment, after determining the target dynamics model of the target protein molecule, an atomic chain composed of a target number of atoms can be further determined in the target dynamics model, which is referred to as the target atomic chain in this embodiment. It is understood that in this embodiment, each atom of the target atomic chain can be stored in one or more (e.g., 2 or 3 spaces, etc.), and this embodiment does not limit it.

[0045] Optionally, in this embodiment, determining the target atomic chain consisting of a target number of atoms in the target dynamics model may include: obtaining all atomic chains of the target dynamics model and determining the number of atoms contained in each atomic chain; filtering each atomic chain based on the target number to obtain each target atomic chain; wherein the target number is an odd number.

[0046] In an optional implementation of this embodiment, after determining the target dynamics model of the target protein molecule, all atomic chains in the target dynamics can be further obtained. The number of atoms contained in each atomic chain can be 2, 3, 4 or 6, etc., and this embodiment does not limit it.

[0047] Furthermore, each atomic chain can be filtered based on the target number to obtain the target atomic chain; for example, atomic chains with the target number of atoms can be retained, and atomic chains with a number of atoms other than the target number can be deleted; for example, if the target number is 5, then atomic chains with 5 atoms can be retained, and other atomic chains can be deleted.

[0048] For example, Figure 3 This is a schematic diagram of a target atomic chain according to Embodiment 1 of the present invention, wherein each target atomic chain contains 5 atoms, and the atoms form bonding relationships with each other; wherein it includes two sets of dihedral angles. And ψ, each dihedral angle is composed of four atoms, that is The three atoms of angular and the three atoms of ψ are the same, and the bond length between any two atoms does not exceed 2 angstroms.

[0049] Step 130: Determine the target reference atom in each of the target atomic chains, and determine the target block where the target reference atom is located. Based on the target computing unit of the target block, perform the calibration spectrum calculation task of the target atomic chain.

[0050] Optionally, in this embodiment, after determining each target atomic chain, a target reference atom can be further determined in each target atomic chain, and the block where the target reference atom is located can be determined, which is referred to as the reference block in this embodiment; furthermore, the calculation task of the correction spectrum of the target atomic chain can be performed based on the calculation unit of the target block.

[0051] It should be noted that in traditional force fields, such as the CHARMM (Chemistry at HARvard Macromolecular Mechanics) field, dihedral terms are typically used to describe the energy changes in rotation within a molecule. However, for complex biomolecules such as proteins, relying solely on simple dihedral terms is insufficient to accurately describe the interactions between main-chain atoms, especially in... The two key dihedral angles are ψ and φ. Therefore, a correction map (CMAP) is introduced to provide additional corrections.

[0052] In its implementation, CMAP exists as a two-dimensional interpolation table, which defines two adjacent dihedral angles (usually...). Energy correction values ​​for all possible combinations of and ψ; each point represents a specific The energy difference relative to the ideal model under various angle combinations; during molecular dynamics simulations, based on the current protein backbone... Given the angle ψ, query the CMAP table to obtain the corresponding energy correction value and add it to the total energy calculation.

[0053] For example, suppose we are simulating a protein whose main chain dihedral angles are... And ψ = -40°; using the standard parameter set of the CHARMM force field, the fundamental energy contribution can first be calculated; then, by looking up the pre-calculated CMAP table, the corresponding... The energy correction value for the position ψ = -40° is calculated and added to the total energy.

[0054] This approach can effectively improve simulation results, making the predicted protein structure closer to experimental data. For example, when simulating secondary structures such as α-helices or β-sheets, CMAP can more accurately reflect the subtle energy changes present in these structures, thereby improving the accuracy of the simulation. Therefore, how to implement CMAP calculations is an important issue in molecular dynamics simulations.

[0055] Optionally, in this embodiment, determining the target reference atom in each of the target atomic chains may include: determining an intermediate atom in the first target atomic chain and determining the intermediate atom as the target reference atom of the first target atomic chain.

[0056] The first target atomic chain can be any target atomic chain, and this embodiment does not limit it.

[0057] Optionally, in this embodiment, after obtaining each target atomic chain, the intermediate atoms of each target atomic chain can be further determined, and each intermediate atom can be designated as the target reference atom of each target atomic chain; for example, Figure 4 This is a schematic diagram of the target reference atom in the target atom chain provided in Embodiment 1 of the present invention.

[0058] The advantage of this setup is that each set of calibration spectra calculations requires information from five atoms as input, and the furthest distance between the innermost atom and other atoms will not exceed two bond lengths, i.e., a maximum of 4 angstroms. This reduces the transmission range for each calibration spectra calculation.

[0059] Furthermore, after determining the intermediate atom as the target reference atom of the first target atomic chain, the method may further include: transferring the offset index of the first block containing other atoms in the first target atomic chain relative to the target block containing the target reference atom, and the atomic position index of each of the first blocks to the target reference atom.

[0060] In other words, in this embodiment, the target reference atom stores the calculation parameters of the calibration spectrum calculation task of the first target atom chain, the offset index of the first block where other atoms in the first target atom chain are located relative to the target block where the target reference atom is located, and the atom position index of each first block.

[0061] In an optional implementation of this embodiment, after determining each target reference atom, the offset index of the block containing the other four atoms in the first target atom chain (referred to as the first block in this embodiment) relative to the target block containing the target reference atom, as well as the atom position index of each first block, can be transmitted to the target reference atom so that the target reference atom can perform subsequent calculations based on this information.

[0062] Optionally, in this embodiment, the target calculation component based on the target block performs the calibration spectrum calculation task of the target atomic chain, which may include: the target calculation component calculates the pressure, potential energy, and force of each atom in the first target atomic chain based on the calculation parameters of the calibration spectrum, the offset index of the first block where other atoms in the first target atomic chain are located relative to the target block where the target reference atom is located, and the atomic position index of each first block;

[0063] The force on the target reference atom is directly added to the information of the target reference atom; the force on each other atom is sent to the relevant atom and added to the atomic information of the relevant atom.

[0064] In an optional implementation of this embodiment, the target reference atom can be calculated based on the calculation parameters of the correction spectrum, the offset index of the first block where other atoms in the first target atom chain are located relative to the target block where the target reference atom is located, and the atom position index of each of the first blocks, thereby obtaining the pressure, potential energy, and force of each atom in the first target atom chain; further, the calculated force of the target reference atom can be accumulated into the information of the target reference atom; the forces of other atoms are sent to the relevant atoms respectively, and further, the relevant forces are accumulated into the atomic information of the relevant atoms.

[0065] It should be noted that for the computational components in the target space, corresponding storage space needs to be reserved based on the maximum number of calibration spectrum computation tasks that each atom may undertake. As can be seen from the list of calibration spectrum atom IDs (Unique Identifiers) in the molecular dynamics system, the IDs of the innermost atom are unique. Therefore, when assigning calibration spectrum computation tasks to the innermost atom, it can be guaranteed that each atom may be assigned no more than one set of calibration spectrum tasks. This saves the reserved storage space for the computational components.

[0066] For example, Table 1 lists the atom IDs for the calibration map calculation task.

[0067] Table 1

[0068]

[0069] In this embodiment, in each computing unit, if an atom carries out the task of calculating the calibration spectrum, the information of the other four atoms stored in that atom is transmitted from the surrounding computing units. The pressure, potential energy, and forces on each atom in the calibration spectrum are then calculated using the following formulas. The forces on the reference atom are directly added to the information of that reference atom, while the forces on the other four atoms are sent back to the computing unit where that atom is located and then added to the corresponding atom information.

[0070] Step 140: In response to the completion instructions of the calculation tasks of each of the target atomic chains, obtain the calculation results of the calibration map of the target protein molecule.

[0071] Optionally, in this embodiment, once the calculation task for all target atomic chains in the target dynamics model is completed, the calculation result of the calibration spectrum of the target protein molecule can be obtained.

[0072] The technical solution of this embodiment obtains a target dynamic model of the target protein molecule by performing dynamic simulation on the target protein molecule. The target dynamic model consists of multiple blocks, and each block contains atoms. A target atomic chain consisting of a target number of atoms is determined in the target dynamic model. A target reference atom is determined in each target atomic chain, and the target block containing the target reference atom is identified. A target computing unit based on the target block executes a calibration spectrum calculation task for the target atomic chain. In response to the completion instruction of the calculation task for each target atomic chain, the calculation result of the calibration spectrum of the target protein molecule is obtained. This enables the calculation of the calibration spectrum of the protein structure, helping to ensure that the force field can more accurately reproduce the quantum-derived potential energy surface and maintain the true protein conformation over time.

[0073] Example 2

[0074] Figure 5 This is a flowchart of a method for calculating a calibration spectrum according to Embodiment 2 of the present invention. This embodiment is a further refinement of the above technical solution, and the technical solution in this embodiment can be combined with various optional solutions in one or more of the above embodiments. Figure 5 As shown, the method includes:

[0075] Step 510: Perform dynamic simulation on the target protein molecule to obtain the target dynamic model of the target protein molecule.

[0076] Optionally, in this embodiment, performing a dynamic simulation on the target protein molecule to obtain a target dynamic model of the target protein molecule may include: obtaining the target protein molecule structure and determining the dynamic simulation conditions; the dynamic simulation conditions include at least one of the following: time step, temperature, and pressure; and performing a dynamic simulation on the target protein molecule structure based on the dynamic simulation conditions to obtain the target dynamic model.

[0077] In an optional implementation of this embodiment, in the process of determining the target dynamics model of the target protein molecule, the structure of the target protein molecule can be obtained first, and the dynamics simulation conditions can be determined. For example, the dynamics simulation conditions input by the user can be obtained through an input interface. Furthermore, the target protein molecule structure can be dynamically simulated based on the dynamics simulation conditions to obtain the target dynamics model.

[0078] Step 520: Determine the target atomic chain consisting of the target number of atoms in the target dynamics model.

[0079] Step 530: Determine the target reference atom in each of the target atom chains, and determine the target block where the target reference atom is located.

[0080] Step 540: The target computing component based on the target block performs the calibration spectrum calculation task of the target atomic chain.

[0081] In this embodiment, the process by which the target computing unit performs the calibration spectrum calculation task of the target atomic chain can be as follows: wherein the calibration spectrum calculation task includes 16 parameters C. ij This corresponds to the grid points on the energy-corrected two-dimensional array. Then, for... Construct a continuous function with angle ψ:

[0082]

[0083] Where, Φ L and ψL It is a reference angle, Δ Φ and Δ ψ It is the correction length.

[0084] Understandably, what was obtained That is, the potential energy V of the calibration spectrum CMAP Regarding the potential energy V CMAP The force exerted by the correction spectrum can be obtained by differentiating relative to the position:

[0085] Ultimately, it can be based on get Thus, the pressure in each direction is obtained:

[0086]

[0087] Step 550: In response to the completion instructions of the computational tasks for each of the target atomic chains, obtain the calculation results of the calibration map of the target protein molecule.

[0088] Optionally, in this embodiment, after the computational task of each target atomic chain is completed, the computational result of the calibration map task of each target atomic chain is determined as the computational result of the calibration map of the target protein molecule.

[0089] The solution of this invention, based on the inherent characteristics of the atom list of the calibration spectrum, assigns the computational task to a specified atom, and combines data transmission within a limited range in three-dimensional space to realize the computation of the calibration spectrum; it can significantly reduce the transmission range between computational components and the storage space reserved by the computational components, thereby improving computational efficiency; this solution has strong adaptability and can be implemented in the computation of arbitrary force fields in molecular dynamics.

[0090] Example 3

[0091] Figure 6 This is a schematic diagram of the structure of a calculation device for a calibration spectrum according to Embodiment 3 of the present invention. Figure 6 As shown, the device includes: a kinetic simulation module 610, a target atomic chain determination module 620, a calibration spectrum calculation task execution module 630, and a calculation result determination module 640.

[0092] The dynamics simulation module 610 is used to perform dynamics simulation on the target protein molecule to obtain a target dynamics model of the target protein molecule; wherein the target dynamics model is composed of multiple blocks, and each block contains atoms;

[0093] The target atomic chain determination module 620 is used to determine the target atomic chain composed of a target number of atoms in the target dynamics model.

[0094] The calibration spectrum calculation task execution module 630 is used to determine the target reference atom in each of the target atomic chains, and determine the target block where the target reference atom is located, and execute the calibration spectrum calculation task of the target atomic chain based on the target calculation unit of the target block;

[0095] The calculation result determination module 640 is used to obtain the calculation result of the calibration map of the target protein molecule in response to the completion instruction of the calculation task of each target atomic chain.

[0096] In this embodiment, a dynamic simulation module performs dynamic simulation on a target protein molecule to obtain a target dynamic model of the target protein molecule. This target dynamic model consists of multiple blocks, each containing atoms. A target atomic chain determination module determines a target atomic chain composed of a target number of atoms within the target dynamic model. A calibration spectrum calculation task execution module determines a target reference atom in each target atomic chain and identifies the target block containing the target reference atom. Based on the target calculation unit of the target block, a calibration spectrum calculation task for the target atomic chain is executed. A calculation result determination module, responding to the completion instructions of the calculation tasks for each target atomic chain, obtains the calculation results of the calibration spectrum of the target protein molecule. This enables the calculation of the calibration spectrum of the protein structure, helping to ensure that the force field can more accurately reproduce the quantum-derived potential energy surface and maintain the true protein conformation over time.

[0097] In an optional implementation of this embodiment, the dynamic simulation module 610 is specifically used for

[0098] Obtain the molecular structure of the target protein and determine the kinetic simulation conditions; the kinetic simulation conditions include at least one of the following: time step, temperature, and pressure;

[0099] Based on the aforementioned kinetic simulation conditions, the molecular structure of the target protein is subjected to kinetic simulation to obtain the target kinetic model.

[0100] In an optional implementation of this embodiment, the target atom chain determination module 620 is specifically used for:

[0101] Obtain all atomic chains of the target dynamic model and determine the number of atoms contained in each atomic chain;

[0102] Each of the atomic chains is filtered based on the target number to obtain the target atomic chains;

[0103] The number of targets is an odd number.

[0104] In an optional implementation of this embodiment, the calibration map calculation task execution module 630 is specifically used for:

[0105] Identify the intermediate atom in the first target atomic chain, and designate the intermediate atom as the target reference atom of the first target atomic chain.

[0106] In an optional implementation of this embodiment, the calculation device for correcting the spectrum further includes: a data transmission module, used for:

[0107] The offset index of the first block containing other atoms in the first target atomic chain relative to the target block containing the target reference atom, and the atomic position index of each first block are transmitted to the target reference atom.

[0108] In an optional implementation of this embodiment, the calibration map calculation task execution module 630 is further specifically used for:

[0109] The target calculation component calculates the pressure, potential energy, and force of each atom in the first target atomic chain based on the calculation parameters of the calibration spectrum, the offset index of the first block where other atoms in the first target atomic chain are located relative to the target block where the target reference atom is located, and the atomic position index of each first block.

[0110] The force on the target reference atom is directly added to the information of the target reference atom; the force on each other atom is sent to the relevant atom and added to the atomic information of the relevant atom.

[0111] The method for calculating the calibration spectrum according to claim 1, characterized in that the calculation result determination module 640 is specifically used for:

[0112] After the computational tasks for each target atomic chain are completed, the computational results of the calibration map tasks for each target atomic chain are determined as the computational results of the calibration map of the target protein molecule.

[0113] The calibration spectrum calculation device provided in the embodiments of the present invention can execute the calibration spectrum calculation method provided in any embodiment of the present invention, and has the corresponding functional modules and beneficial effects of the execution method.

[0114] In the technical solutions of the embodiments of the present invention, the collection, storage, use, processing, transmission, provision and disclosure of protein molecules (e.g., analytical structures, dynamic models, etc.) all comply with the provisions of relevant laws and regulations and do not violate public order and good morals.

[0115] Example 4

[0116] Figure 7A schematic diagram of an electronic device 10 that can be used to implement embodiments of the present invention is shown. The electronic device is intended to represent various forms of digital computers, such as laptop computers, desktop computers, workstations, personal digital assistants, servers, blade servers, mainframe computers, and other suitable computers. The electronic device can also represent various forms of mobile devices, such as personal digital processors, cellular phones, smartphones, wearable devices (e.g., helmets, glasses, watches, etc.), and other similar computing devices. The components shown herein, their connections and relationships, and their functions are merely illustrative and are not intended to limit the implementation of the invention described and / or claimed herein.

[0117] like Figure 7 As shown, the electronic device 10 includes at least one processor 11 and a memory, such as a read-only memory (ROM) 12 or a random access memory (RAM) 13, communicatively connected to the at least one processor 11. The memory stores computer programs executable by the at least one processor. The processor 11 can perform various appropriate actions and processes based on the computer program stored in the ROM 12 or loaded from storage unit 18 into the RAM 13. The RAM 13 may also store various programs and data required for the operation of the electronic device 10. The processor 11, ROM 12, and RAM 13 are interconnected via a bus 14. An input / output (I / O) interface 15 is also connected to the bus 14.

[0118] Multiple components in electronic device 10 are connected to I / O interface 15, including: input unit 16, such as keyboard, mouse, etc.; output unit 17, such as various types of displays, speakers, etc.; storage unit 18, such as disk, optical disk, etc.; and communication unit 19, such as network card, modem, wireless transceiver, etc. Communication unit 19 allows electronic device 10 to exchange information / data with other devices through computer networks such as the Internet and / or various telecommunications networks.

[0119] Processor 11 can be various general-purpose and / or special-purpose processing components with processing and computing capabilities. Some examples of processor 11 include, but are not limited to, central processing unit (CPU), graphics processing unit (GPU), various special-purpose artificial intelligence (AI) computing chips, various processors running machine learning model algorithms, digital signal processors (DSP), and any suitable processor, controller, microcontroller, etc. Processor 11 executes the various methods and processes described above, such as a method for calculating a calibration spectrum, which may include: performing a dynamic simulation of a target protein molecule to obtain a target dynamic model of the target protein molecule; wherein the target dynamic model consists of multiple blocks, and each block contains atoms; determining a target atomic chain consisting of a target number of atoms in the target dynamic model; determining a target reference atom in each of the target atomic chains and determining the target block in which the target reference atom is located; performing a calibration spectrum calculation task of the target atomic chain based on a target computing component of the target block; and obtaining the calculation result of the calibration spectrum of the target protein molecule in response to a completion instruction for the calculation task of each of the target atomic chains.

[0120] In some embodiments, the method for calculating the calibration spectrum may be implemented as a computer program tangibly contained in a computer-readable storage medium, such as storage unit 18. In some embodiments, part or all of the computer program may be loaded and / or installed on electronic device 10 via ROM 12 and / or communication unit 19. When the computer program is loaded into RAM 13 and executed by processor 11, one or more steps of the method for calculating the calibration spectrum described above may be performed. Alternatively, in other embodiments, processor 11 may be configured to perform the method for calculating the calibration spectrum by any other suitable means (e.g., by means of firmware).

[0121] Various embodiments of the systems and techniques described above herein can be implemented in digital electronic circuit systems, integrated circuit systems, field-programmable gate arrays (FPGAs), application-specific integrated circuits (ASICs), application-specific standard products (ASSPs), systems-on-a-chip (SoCs), payload-programmable logic devices (CPLDs), computer hardware, firmware, software, and / or combinations thereof. These various embodiments may include implementations in one or more computer programs that can be executed and / or interpreted on a programmable system including at least one programmable processor, which may be a dedicated or general-purpose programmable processor, capable of receiving data and instructions from a storage system, at least one input device, and at least one output device, and transmitting data and instructions to the storage system, the at least one input device, and the at least one output device.

[0122] Computer programs used to implement the methods of the present invention may be written in any combination of one or more programming languages. These computer programs may be provided to a processor of a general-purpose computer, a special-purpose computer, or other programmable data processing device, such that when executed by the processor, the computer programs cause the functions / operations specified in the flowcharts and / or block diagrams to be performed. The computer programs may be executed entirely on a machine, partially on a machine, or as a standalone software package, partially on a machine and partially on a remote machine, or entirely on a remote machine or server.

[0123] In the context of this invention, a computer-readable storage medium can be a tangible medium that may contain or store a computer program for use by or in conjunction with an instruction execution system, apparatus, or device. A computer-readable storage medium may include, but is not limited to, electronic, magnetic, optical, electromagnetic, infrared, or semiconductor systems, apparatus, or devices, or any suitable combination thereof. Alternatively, a computer-readable storage medium may be a machine-readable signal medium. More specific examples of machine-readable storage media include electrical connections based on one or more wires, portable computer disks, hard disks, random access memory (RAM), read-only memory (ROM), erasable programmable read-only memory (EPROM or flash memory), optical fibers, portable compact disk read-only memory (CD-ROM), optical storage devices, magnetic storage devices, or any suitable combination thereof.

[0124] To provide interaction with a user, the systems and techniques described herein can be implemented on an electronic device having: a display device (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor) for displaying information to the user; and a keyboard and pointing device (e.g., a mouse or trackball) through which the user provides input to the electronic device. Other types of devices can also be used to provide interaction with the user; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user can be received in any form (including sound input, voice input, or tactile input).

[0125] The systems and technologies described herein can be implemented in computing systems that include backend components (e.g., as data servers), or computing systems that include middleware components (e.g., application servers), or computing systems that include frontend components (e.g., user computers with graphical user interfaces or web browsers through which users can interact with implementations of the systems and technologies described herein), or any combination of such backend, middleware, or frontend components. The components of the system can be interconnected via digital data communication of any form or medium (e.g., communication networks). Examples of communication networks include local area networks (LANs), wide area networks (WANs), blockchain networks, and the Internet.

[0126] A computing system can include clients and servers. Clients and servers are generally located far apart and typically interact through communication networks. The client-server relationship is created by computer programs running on the respective computers and having a client-server relationship with each other. The server can be a cloud server, also known as a cloud computing server or cloud host, which is a hosting product within the cloud computing service system to address the shortcomings of traditional physical hosts and VPS services, such as high management difficulty and weak business scalability.

[0127] It should be understood that the various forms of processes shown above can be used, with steps reordered, added, or deleted. For example, the steps described in this invention can be executed in parallel, sequentially, or in different orders, as long as the desired result of the technical solution of this invention can be achieved, and this is not limited herein.

[0128] The specific embodiments described above do not constitute a limitation on the scope of protection of this invention. Those skilled in the art should understand that various modifications, combinations, sub-combinations, and substitutions can be made according to design requirements and other factors. Any modifications, equivalent substitutions, and improvements made within the spirit and principles of this invention should be included within the scope of protection of this invention.

[0129] This invention also provides a computer program product, including a computer program that, when executed by a processor, implements a database detection method as provided in any embodiment of this application.

[0130] In implementing the computer program product, computer program code for performing the operations of this invention can be written in one or more programming languages ​​or a combination thereof. Programming languages ​​include object-oriented programming languages ​​such as Java, Smalltalk, and C++, as well as conventional procedural programming languages ​​such as C or similar languages. The program code can be executed entirely on the user's computer, partially on the user's computer, as a standalone software package, partially on the user's computer and partially on a remote computer, or entirely on a remote computer or server. In cases involving remote computers, the remote computer can be connected to the user's computer via any type of network—including a local area network (LAN) or a wide area network (WAN)—or can be connected to an external computer (e.g., via the Internet using an Internet service provider).

[0131] It should be noted that in the embodiments of this application, certain software, components, models and other existing solutions in the industry may be mentioned. These should be regarded as exemplary and are only intended to illustrate the feasibility of implementing the technical solution of this application. However, it does not mean that the applicant has used or necessarily used the solution.

[0132] Note that the above description is merely a preferred embodiment of the present invention and the technical principles employed. Those skilled in the art will understand that the present invention is not limited to the specific embodiments described herein, and various obvious changes, readjustments, and substitutions can be made without departing from the scope of protection of the present invention. Therefore, although the present invention has been described in detail through the above embodiments, the present invention is not limited to the above embodiments, and may include many other equivalent embodiments without departing from the concept of the present invention, the scope of which is determined by the scope of the appended claims.

Claims

1. A method for calculating a calibration spectrum, characterized in that, include: A dynamic simulation of the target protein molecule is performed to obtain a target dynamic model of the target protein molecule; wherein the target dynamic model is composed of multiple blocks, and each block contains atoms; In the target dynamics model, a target atomic chain consisting of a target number of atoms is determined; In each of the target atomic chains, a target reference atom is determined, and the target block in which the target reference atom is located is determined. Based on the target computing unit of the target block, the calibration spectrum calculation task of the target atomic chain is performed. In response to the completion instructions of the computational tasks of each of the target atomic chains, the calculation results of the calibration map of the target protein molecule are obtained.

2. The method for calculating the calibration spectrum according to claim 1, characterized in that, The process of performing dynamic simulations on the target protein molecule to obtain a target dynamic model of the target protein molecule includes: Obtain the molecular structure of the target protein and determine the kinetic simulation conditions; the kinetic simulation conditions include at least one of the following: time step, temperature, and pressure; Based on the aforementioned kinetic simulation conditions, the molecular structure of the target protein is subjected to kinetic simulation to obtain the target kinetic model.

3. The method for calculating the calibration spectrum according to claim 1, characterized in that, Determining the target atomic chain consisting of a target number of atoms in the target dynamics model includes: Obtain all atomic chains of the target dynamic model and determine the number of atoms contained in each atomic chain; Each of the atomic chains is filtered based on the target number to obtain the target atomic chains; The number of targets is an odd number.

4. The method for calculating the calibration spectrum according to claim 3, characterized in that, The step of determining the target reference atom in each of the target atom chains includes: Identify the intermediate atom in the first target atomic chain, and designate the intermediate atom as the target reference atom of the first target atomic chain.

5. The method for calculating the calibration spectrum according to claim 4, characterized in that, After identifying the intermediate atom as the target reference atom of the first target atom chain, the method further includes: The offset index of the first block containing other atoms in the first target atomic chain relative to the target block containing the target reference atom, and the atomic position index of each first block are transmitted to the target reference atom.

6. The method for calculating the calibration spectrum according to claim 5, characterized in that, The target computing component based on the target block performs the calibration spectrum calculation task of the target atomic chain, including: The target calculation component calculates the pressure, potential energy, and force of each atom in the first target atomic chain based on the calculation parameters of the calibration spectrum, the offset index of the first block where other atoms in the first target atomic chain are located relative to the target block where the target reference atom is located, and the atomic position index of each first block. The force on the target reference atom is directly added to the information of the target reference atom; the force on each other atom is sent to the relevant atom and added to the atomic information of the relevant atom.

7. The method for calculating the calibration spectrum according to claim 1, characterized in that, The calculation results of obtaining the corrected spectrum of the target protein molecule in response to the completion instructions of the computational tasks of each of the target atomic chains include: After the computational tasks for each target atomic chain are completed, the computational results of the calibration map tasks for each target atomic chain are determined as the computational results of the calibration map of the target protein molecule.

8. An electronic device, characterized in that, The electronic device includes: At least one processor; and A memory communicatively connected to the at least one processor; wherein, The memory stores a computer program that can be executed by the at least one processor, the computer program being executed by the at least one processor to enable the at least one processor to perform the calculation method of the calibration spectrum according to any one of claims 1-7.

9. A computer-readable storage medium, characterized in that, The computer-readable storage medium stores computer instructions that, when executed by a processor, implement the method for calculating the calibration spectrum according to any one of claims 1-7.

10. A computer program product comprising a computer program that, when executed by a processor, implements the method for calculating the calibration spectrum according to any one of claims 1-7.

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