Atomic recognition and selection method and device, server, storage medium and product

Abstract

The invention provides an atom identification and selection method and device, a server, a storage medium and a product, and the method comprises the steps: obtaining the atom attribution information and atom coordinates of all atoms, determining a ligand atom and a receptor atom, and calculating the position coordinates of the centroid of the ligand; determining a candidate ligand atom; selecting a first special atom P1 and a second special atom P2; selecting a third special atom P3 according to a first preset screening rule; determining candidate receptor atoms; a fourth special atom P4 is selected; and selecting a fifth special atom P5 and a sixth special atom P6 according to a second preset screening rule. The atom recognition and selection method and device, the server, the storage medium and the product provided by the invention can replace manual selection of special atoms between the ligand and the receptor, so that the workload of workers is reduced, and the screening efficiency of the special atoms is improved.

Description

Technical Field

[0001] The present invention relates to the field of molecular simulation computing technology, and in particular to a method, device, server, storage medium and product for identifying and selecting atoms. Background Art

[0002] Over the past century, small molecule drugs have represented the dominant model of drug research, achieving medical breakthroughs and saving countless lives. Small molecules achieve therapeutic effects by binding to target proteins, inhibiting protein function, or regulating key cell signaling pathways by inducing protein conformational changes. Researchers use different methods to calculate and simulate the binding process between ligands and target proteins, such as free energy perturbation calculations (FEP), which predict the binding affinity of small molecules with their protein partners by measuring the strength of the interaction between the two molecules, greatly improving the success rate of preclinical drug discovery, thereby identifying higher quality development candidates for clinical testing. The RED (Restraint Energy Distribution) method, which adds a bonding-like restriction method between the ligand and the receptor protein, can reduce the activity space between the ligand and the receptor protein, indirectly reducing the sampling space of the molecular dynamics simulation, thereby helping researchers effectively reduce the time of computational simulation. However, when using the RED method, some special atoms need to be selected to form a bonded structure. In the prior art, the process of determining special atoms requires staff to manually observe the topological structures of ligands and receptors and determine them one by one according to certain rules. Therefore, when there are many ligand and receptor protein samples, it will not only lead to a significant increase in the workload of the staff, but also reduce the screening efficiency of special atoms. Summary of the invention

[0003] In view of this, the present invention aims to propose an atom identification and selection method, device, server, storage medium and product to solve the above-mentioned technical problems.

[0004] To achieve the above object, the technical solution created by the present invention is implemented as follows:

[0005] In a first aspect, an embodiment of the present invention provides an atom identification and selection method, comprising:

[0006] Obtaining atomic attribution information and atomic coordinates of all atoms, classifying all atoms according to the atomic attribution information, determining ligand atoms and receptor atoms, and calculating the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms;

[0007] Obtain the relative atomic mass of the ligand atom, screen the ligand atom according to the relative atomic mass, and determine the candidate ligand atom;

[0008] The distance from each candidate ligand atom to the ligand centroid is calculated according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, the candidate ligand atom closest to the ligand centroid is selected as the first special atom P1, and the candidate ligand atom farthest from the ligand centroid is selected as the second special atom P2;

[0009] Screening other candidate ligand atoms according to the first preset screening rule, and selecting the third special atom P3;

[0010] Obtaining the atomic names of the receptor atoms, screening the receptor atoms according to the atomic names, and determining candidate receptor atoms;

[0011] The distance between each candidate receptor atom and the ligand centroid is calculated according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and the candidate receptor atom closest to the ligand centroid is selected as the fourth special atom P4;

[0012] The amino acid where the fourth special atom P4 is located is determined according to the atom attribution information of the fourth special atom P4, and other acceptor atoms in the amino acid are screened according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

[0013] Furthermore, the atomic coordinates are obtained by parsing the gro file of the molecular dynamics simulation system, and the atomic attribution information, the relative atomic mass of the ligand atoms and the atomic names of the receptor atoms are all obtained by parsing the top file of the molecular dynamics simulation system.

[0014] Furthermore, the screening of ligand atoms according to relative atomic mass to determine candidate ligand atoms includes:

[0015] When the relative atomic mass of a ligand atom is greater than 4, the ligand atom is determined as a candidate ligand atom.

[0016] Furthermore, the step of screening other candidate ligand atoms according to the first preset screening rule to select the third special atom P3 includes:

[0017] Calculate the distance L12 between the first special atom P1 and the second special atom P2;

[0018] The other candidate ligand atoms are sorted according to the distances from the other candidate ligand atoms to the ligand centroid, and the candidate ligand atoms are substituted into the following formula one by one according to the sorting for verification:

[0019] 0>(L12*L12+L1X*L1X-L2X*L2X) / (2*L12*L1X)

[0020] Wherein, L1X is the distance from other candidate ligand atoms to the first special atom P1, and L2X is the distance from other candidate ligand atoms to the second special atom P2;

[0021] When the first candidate ligand atom that makes the above formula valid appears, the candidate ligand atom is determined as the third special atom P3.

[0022] Furthermore, the screening of receptor atoms according to the atom names to determine candidate receptor atoms includes:

[0023] When the atom name of the acceptor atom is CA, the acceptor atom is determined as a candidate acceptor atom.

[0024] Furthermore, the step of screening other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6 comprises:

[0025] obtaining the acceptor atom ordering in the amino acid;

[0026] The last atom named C in the acceptor atom sequence is selected as the fifth special atom P5, and the last atom named O in the acceptor atom sequence is selected as the sixth special atom P6.

[0027] In a second aspect, an embodiment of the present invention provides an atom identification and selection device, comprising:

[0028] A preprocessing module is used to obtain the atomic attribution information and atomic coordinates of all atoms, classify all atoms according to the atomic attribution information, determine the ligand atoms and the receptor atoms, and calculate the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms;

[0029] The first candidate determination module is used to obtain the relative atomic mass of the ligand atom, screen the ligand atom according to the relative atomic mass, and determine the candidate ligand atom;

[0030] A first calculation module is used to calculate the distance from each candidate ligand atom to the ligand centroid according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, select the candidate ligand atom closest to the ligand centroid as the first special atom P1, and select the candidate ligand atom farthest from the ligand centroid as the second special atom P2;

[0031] A first screening module, used to screen other candidate ligand atoms according to a first preset screening rule and select a third special atom P3;

[0032] The second candidate determination module is used to obtain the atomic names of the receptor atoms, screen the receptor atoms according to the atomic names, and determine the candidate receptor atoms;

[0033] The second calculation module is used to calculate the distance between each candidate receptor atom and the ligand centroid according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and select the candidate receptor atom closest to the ligand centroid as the fourth special atom P4;

[0034] The second screening module is used to determine the amino acid where the fourth special atom P4 is located according to the atom attribution information of the fourth special atom P4, and screen other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

[0035] In a third aspect, an embodiment of the present invention provides a server, including:

[0036] one or more processors;

[0037] A storage device for storing one or more programs;

[0038] When the one or more programs are executed by the one or more processors, the one or more processors implement the atom identification and selection method provided in the above embodiment.

[0039] In a fourth aspect, an embodiment of the present invention further provides a storage medium comprising computer executable instructions, which, when executed by a computer processor, are used to execute the atom identification and selection method provided in the above embodiment.

[0040] In a fifth aspect, an embodiment of the present invention further provides a computer program product, wherein the computer program product stores at least one program code, and the at least one program code is used to be executed by a processor to implement the atom identification and selection method provided in the above embodiment.

[0041] Compared with the prior art, the atom identification and selection method, device, server, storage medium and product of the present invention have the following advantages:

[0042] The present invention creates a method, device, server, storage medium and product for atomic identification and selection, which can divide atoms into ligand atoms and receptor atoms through atomic attribution information, calculate the position coordinates of the ligand centroid through atomic coordinates, and determine candidate ligand atoms and candidate receptor atoms according to the relative atomic mass of the ligand atom and the atomic name of the receptor atom. Subsequently, the present invention can also select the first special atom P1, the second special atom P2 and the third special atom P3 according to the distance relationship between the candidate ligand atom and the ligand centroid, so that the first special atom P1, the second special atom P2 and the third special atom P3 can fully reflect the spatial shape of the ligand. In addition, the present invention can also select the fourth special atom P4, the fifth special atom P5 and the sixth special atom P6 according to the atomic type and actual position of the candidate receptor atom, so as to facilitate the use of special atoms to form a bonded structure in the subsequent RED processing process. Compared with the prior art, the present invention can replace manual selection of special atoms between ligands and receptors, thereby reducing the workload of staff and improving the screening efficiency of special atoms. BRIEF DESCRIPTION OF THE DRAWINGS

[0043] In order to more clearly illustrate the technical solutions in the embodiments of the present disclosure, the drawings required for use in the description of the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present disclosure. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0044] Figure 1 A flowchart of the atom identification and selection method described in Example 1 of the present invention is created;

[0045] Figure 2 This is a schematic diagram of the structure of the atom identification and selection device described in the second embodiment of the present invention;

[0046] Figure 3 This is a structural diagram of the server described in Example 3 of the present invention. DETAILED DESCRIPTION

[0047] The present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments. It is to be understood that the specific embodiments described herein are only used to explain the present invention, rather than to limit the present invention. It should also be noted that, for ease of description, only parts related to the present invention, rather than all structures, are shown in the accompanying drawings.

[0048] Embodiment 1

[0049] Figure 1 : is a flow chart of an atom identification and selection method provided in Embodiment 1 of the present invention. As shown in the figure, the atom identification and selection method specifically includes the following steps:

[0050] Step 110, obtaining the atomic attribution information and atomic coordinates of all atoms, classifying all atoms according to the atomic attribution information, determining ligand atoms and receptor atoms, and calculating the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms.

[0051] In the process of developing small molecule drugs, staff usually perform free energy perturbation calculations in molecular dynamics simulation systems, and use the RED method to select specific atoms in ligands and receptor proteins to add bonded-like restraint structures, thereby reducing the sampling space of molecular dynamics simulations and the overall amount of calculations. However, when there are many ligand and receptor protein samples, the workload of manual screening by staff will increase, thus affecting the identification and screening efficiency of specific atoms.

[0052] To solve this problem, this embodiment will obtain the atomic identification information and atomic coordinates of all atoms in the molecular dynamics simulation system before identifying and selecting atoms, so as to classify all atoms according to the atomic identification information, determine the ligand atoms and receptor atoms, and calculate the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms, so as to facilitate subsequent processing.

[0053] It should be noted that in order to conveniently obtain the atomic attribution information and atomic coordinates of all atoms in the molecular dynamics simulation system, the gro file and top file of the molecular dynamics simulation system can be parsed, so as to determine the atomic coordinates through the parsing results of the gro file, and determine the atomic attribution information through the parsing results of the top file.

[0054] Step 120: Obtain the relative atomic mass of the ligand atom, screen the ligand atom according to the relative atomic mass, and determine the candidate ligand atom.

[0055] Since there are many types of ligand atoms in the ligand, when selecting the special atoms required by the RED method in the ligand, it is necessary to identify and judge the type of atoms to ensure that the selected special atoms in the ligand can fully reflect the spatial shape of the ligand and facilitate the use of special atoms for subsequent bonded-like structure addition.

[0056] In this embodiment, the relative atomic mass of the ligand atom is used to assist in determining the type of the ligand atom. It should be noted that the relative atomic mass of the ligand atom can be obtained by analyzing the top file of the molecular dynamics simulation system.

[0057] After obtaining the relative atomic mass of the ligand atom, the relative atomic mass threshold can be set according to the actual situation, and the ligand atoms can be screened by the relative atomic mass threshold, so as to determine the ligand atoms that meet the special atomic requirements as candidate ligand atoms.

[0058] Optionally, the ligand atoms are screened according to the relative atomic mass to determine the candidate ligand atoms, which can be specifically optimized as follows:

[0059] When the relative atomic mass of a ligand atom is greater than 4, the ligand atom is determined as a candidate ligand atom.

[0060] When the relative atomic mass of a ligand atom is greater than 4, it can be determined that the ligand atom must be a non-hydrogen atom. At this time, the atom meets the requirements of being a special atom in the ligand, so the ligand atom can be determined as a candidate ligand atom.

[0061] Step 130, calculate the distance from each candidate ligand atom to the ligand centroid according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, select the candidate ligand atom closest to the ligand centroid as the first special atom P1, and select the candidate ligand atom farthest from the ligand centroid as the second special atom P2.

[0062] Since the special atoms selected in the ligand need to fully reflect the spatial shape of the ligand, when selecting special atoms from the candidate ligand atoms, it should be ensured that the special atoms are evenly distributed in the ligand centroid and edge area. In view of this, this embodiment will first calculate the distance from each candidate ligand atom to the ligand centroid through the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid to clarify the position of each candidate ligand atom relative to the ligand centroid, and then select the candidate ligand atom closest to the ligand centroid as the first special atom P1, and select the candidate ligand atom farthest from the ligand centroid as the second special atom P2.

[0063] As an optional implementation of this embodiment, in order to simplify the calculation process of this method, when calculating the distance between the candidate ligand atom and the ligand centroid, the atomic ID of the candidate ligand atom can be used as the imaginary part of the complex number, and the distance between the candidate ligand atom and the ligand centroid can be used as the real part of the complex number, thereby generating a complex number, and defining a sorting comparison function based on the complex number. In this case, the distance ranking between each candidate ligand atom and the ligand centroid can be accurately obtained through the sorting comparison function, and the additional setting of the structure can be avoided, thereby simplifying the calculation process of this method.

[0064] Step 140: Screen other candidate ligand atoms according to the first preset screening rule and select the third special atom P3.

[0065] Generally, since three special atoms need to be selected in the ligand to fully reflect the spatial shape of the ligand, this embodiment will screen other candidate ligand atoms according to the first preset screening rule based on the first special atom P1 and the second special atom P2, and select the third special atom P3.

[0066] Specifically, screening other candidate ligand atoms according to the first preset screening rule and selecting the third special atom P3 may include:

[0067] Calculate the distance L12 between the first special atom P1 and the second special atom P2;

[0068] The other candidate ligand atoms are sorted according to the distances from the other candidate ligand atoms to the ligand centroid, and the candidate ligand atoms are substituted into the following formula one by one according to the sorting for verification:

[0069] 0>(L12*L12+L1X*L1X-L2X*L2X) / (2*L12*L1X)

[0070] Wherein, L1X is the distance from other candidate ligand atoms to the first special atom P1, and L2X is the distance from other candidate ligand atoms to the second special atom P2;

[0071] When the first candidate ligand atom that makes the above formula valid appears, the cosine theorem can prove that the angle formed by the candidate ligand atom and the second special atom P2 with the first special atom P1 as the vertex is greater than 90 degrees. At this time, the candidate ligand atom can be determined as the third special atom P3, so that the spatial shape of the ligand is fully reflected by the first special atom P1, the second special atom P2 and the third special atom P3.

[0072] It should be noted that when calculating L12, L1X and L2X, the calculation should be performed based on the atomic coordinates of the first special atom P1, the second special atom P2 and other candidate ligand atoms.

[0073] Since the first preset screening rule will first sort the other candidate ligand atoms according to the distance between them and the ligand centroid, and substitute the other candidate ligand atoms into the formula one by one for verification according to the sorting, it can not only reduce the overall amount of calculation in the actual calculation process and avoid all other candidate ligand atoms at once, but also ensure that the selected third special atom P3 has a larger distance from the ligand centroid, thereby better reflecting the spatial shape of the ligand.

[0074] Step 150: Obtain the atomic names of the receptor atoms, screen the receptor atoms according to the atomic names, and determine candidate receptor atoms.

[0075] Generally, the atomic name of the receptor atom can reflect its atomic type. Therefore, in order to ensure that the special atoms selected in the receptor meet the actual usage requirements, the receptor atoms can be screened according to their atomic names to determine the candidate receptor atoms.

[0076] In this embodiment, the receptor atoms are screened according to the atom names to determine the candidate receptor atoms, which can be specifically optimized as follows:

[0077] When the atom name of the acceptor atom is CA, the acceptor atom is determined as a candidate acceptor atom.

[0078] It should be noted that the atomic names of the receptor atoms in this embodiment can also be obtained by parsing the top file of the molecular dynamics simulation system.

[0079] When the atomic name of the receptor atom is CA, it proves that the current receptor atom is an alpha carbon atom. Since the alpha carbon atom is the closest carbon atom connected to the parent functional group in the main chain of organic matter, determining the alpha carbon atom in the receptor atom as a candidate receptor atom can ensure that the subsequent addition of bonded structures can proceed smoothly, thereby achieving a better binding effect between the ligand and the receptor.

[0080] Step 160 , calculating the distance from each candidate receptor atom to the ligand centroid according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and selecting the candidate receptor atom closest to the ligand centroid as the fourth special atom P4.

[0081] After the candidate receptor atoms are determined, this embodiment will calculate the distance from each candidate receptor atom to the centroid of the ligand based on the atomic coordinates of the candidate receptor atom and the position coordinates of the centroid of the ligand, and select the candidate receptor atom closest to the centroid of the ligand as the fourth special atom P4, so as to facilitate the selection of the remaining special atoms in the receptor based on the fourth special atom P4.

[0082] Step 170, determining the amino acid where the fourth special atom P4 is located according to the atom attribution information of the fourth special atom P4, and screening other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

[0083] Since the smallest building block of the receptor protein is amino acid, when selecting other special atoms among the receptor atoms, the amino acid where the fourth special atom P4 is located should be determined first based on the atomic attribution information of the fourth special atom P4, and then the fifth special atom P5 and the sixth special atom P6 should be selected among the amino acids according to the second preset screening rules to ensure that the other special atoms are in the same amino acid as the fourth special atom P4.

[0084] Specifically, screening other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6 may include:

[0085] obtaining the acceptor atom ordering in the amino acid;

[0086] The last atom named C in the acceptor atom sequence is selected as the fifth special atom P5, and the last atom named O in the acceptor atom sequence is selected as the sixth special atom P6.

[0087] In the top file of the molecular dynamics simulation system, the last few atoms in the internal atomic sequence of the amino acid are usually atoms on the carboxyl group, where the atom with the atomic name C is the carbon atom of the carboxyl group, and the atom with the atomic name O is the oxygen atom on the carboxyl group. In this embodiment, the last atom with the atomic name C and the last atom with the atomic name O in the receptor atomic sequence are selected as the fifth special atom P5 and the sixth special atom P6, which not only ensures that all special atoms in the receptor are in the same amino acid, but also makes the fifth special atom P5 and the sixth special atom P6 located under the same residue, thereby improving the binding constraint effect between the receptor and the ligand.

[0088] This embodiment divides atoms into ligand atoms and receptor atoms through atomic attribution information, calculates the position coordinates of the ligand centroid through atomic coordinates, and can determine candidate ligand atoms and candidate receptor atoms according to the relative atomic mass of the ligand atom and the atomic name of the receptor atom. Subsequently, the present invention can also select the first special atom P1, the second special atom P2 and the third special atom P3 according to the distance relationship between the candidate ligand atom and the ligand centroid, so that the first special atom P1, the second special atom P2 and the third special atom P3 can fully reflect the spatial shape of the ligand. In addition, the present invention can also select the fourth special atom P4, the fifth special atom P5 and the sixth special atom P6 according to the atomic type and actual position of the candidate receptor atom, so as to facilitate the use of special atoms to form a bonded structure in the subsequent RED processing process. Compared with the prior art, the present invention can replace manual selection of special atoms between ligands and receptors, thereby reducing the workload of staff and improving the screening efficiency of special atoms.

[0089] Embodiment 2

[0090] Figure 2 Schematic diagram of the structure of the atom identification and selection device provided in the second embodiment of the present invention. Figure 2 As shown, the atom identification and selection device includes:

[0091] A preprocessing module 210 is used to obtain atomic attribution information and atomic coordinates of all atoms, classify all atoms according to the atomic attribution information, determine ligand atoms and receptor atoms, and calculate the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms;

[0092] A first candidate determination module 220 is used to obtain the relative atomic mass of the ligand atoms, screen the ligand atoms according to the relative atomic mass, and determine the candidate ligand atoms;

[0093] A first calculation module 230, for calculating the distance from each candidate ligand atom to the ligand centroid according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, selecting the candidate ligand atom closest to the ligand centroid as the first special atom P1, and selecting the candidate ligand atom farthest from the ligand centroid as the second special atom P2;

[0094] A first screening module 240 is used to screen other candidate ligand atoms according to a first preset screening rule and select a third special atom P3;

[0095] The second candidate determination module 250 is used to obtain the atomic names of the receptor atoms, screen the receptor atoms according to the atomic names, and determine the candidate receptor atoms;

[0096] A second calculation module 260 is used to calculate the distance from each candidate receptor atom to the ligand centroid according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and select the candidate receptor atom closest to the ligand centroid as the fourth special atom P4;

[0097] The second screening module 270 is used to determine the amino acid where the fourth special atom P4 is located according to the atom attribution information of the fourth special atom P4, and screen other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

[0098] The atom recognition and selection device provided in this embodiment can divide atoms into ligand atoms and receptor atoms through a preprocessing module, and determine the position coordinates of the ligand centroid, and can also determine candidate ligand atoms and candidate receptor atoms through a first candidate determination module and a second candidate determination module. Secondly, the device can select the first special atom P1, the second special atom P2 and the fourth special atom P4 through the first calculation module and the second calculation module. In addition, the device can also select the third special atom P3, the fifth special atom P5 and the sixth special atom P6 through the first screening module and the second screening module. Through the cooperation of the above modules, it is possible to replace manual selection of special atoms between ligands and receptors, thereby reducing the workload of staff and improving the screening efficiency of special atoms.

[0099] Based on the above embodiment, the first screening module includes:

[0100] A distance calculation unit, used for calculating a distance L12 between the first special atom P1 and the second special atom P2;

[0101] The verification and screening unit is used to sort other candidate ligand atoms according to the distances from other candidate ligand atoms to the ligand centroid, and substitute the candidate ligand atoms one by one into the following formula for verification according to the sorting:

[0102] 0>(L12*L12+L1X*L1X-L2X*L2X) / (2*L12*L1X)

[0103] Wherein, L1X is the distance from other candidate ligand atoms to the first special atom P1, and L2X is the distance from other candidate ligand atoms to the second special atom P2; when the first candidate ligand atom that makes the above formula valid appears, the candidate ligand atom is determined as the third special atom P3.

[0104] Based on the above embodiment, the second screening module includes:

[0105] A ranking acquisition unit, used to acquire the ranking of acceptor atoms in the amino acid;

[0106] The selection unit is used to select the last atom named C in the acceptor atom sequence as the fifth special atom P5, and to select the last atom named O in the acceptor atom sequence as the sixth special atom P6.

[0107] The atom identification and selection device provided in the embodiment of the present invention can execute the atom identification and selection method provided in any embodiment of the present invention, and has the corresponding functional modules and beneficial effects of the execution method.

[0108] Embodiment 3

[0109] Figure 3 A schematic diagram of the structure of a server provided in Embodiment 3 of the present invention. Figure 3 A block diagram of an exemplary server 12 suitable for use in implementing embodiments of the present invention is shown. Figure 3 The server 12 shown is only an example and should not bring any limitation to the functions and scope of use of the embodiments of the present invention.

[0110] like Figure 3 As shown, the server 12 is in the form of a general purpose computing device. The components of the server 12 may include, but are not limited to: one or more processors or processing units 16, server memory 28, and a bus 18 connecting different server components (including server memory 28 and processing unit 16).

[0111] Bus 18 represents one or more of several types of bus structures, including a memory bus or memory controller, a peripheral bus, an accelerated graphics port, a processor or a local bus using any of a variety of bus architectures. By way of example, these architectures include, but are not limited to, an Industry Standard Architecture (ISA) bus, a Micro Channel Architecture (MAC) bus, an Enhanced ISA bus, a Video Electronics Standards Association (VESA) local bus, and a Peripheral Component Interconnect (PCI) bus.

[0112] The server 12 typically includes a variety of computer server readable media. These media can be any available media that can be accessed by the server 12, including volatile and non-volatile media, removable and non-removable media.

[0113] Server memory 28 may include computer server readable media in the form of volatile memory, such as random access memory (RAM) 30 and / or cache 32. Server 12 may further include other removable / non-removable, volatile / non-volatile computer server storage media. By way of example only, storage server 34 may be used to read and write non-removable, non-volatile magnetic media ( Figure 3 not shown, usually called a "hard drive"). Although Figure 3 Not shown in the figure, a disk drive for reading and writing to a removable non-volatile disk (e.g., a "floppy disk"), and an optical disk drive for reading and writing to a removable non-volatile optical disk (e.g., a CD-ROM, a DVD-ROM, or other optical media) may be provided. In these cases, each drive may be connected to the bus 18 via one or more data medium interfaces. The server memory 28 may include at least one program product having a set (e.g., at least one) of program modules that are configured to perform the functions of various embodiments of the present invention.

[0114] A program / utility 40 having a set (at least one) of program modules 42 may be stored, for example, in the server memory 28, such program modules 42 including, but not limited to, operating a server, one or more application programs, other program modules, and program data, each of which or some combination may include an implementation of a network environment. The program modules 42 generally perform the functions and / or methods of the embodiments described herein.

[0115] The server 12 may also communicate with one or more external devices 14 (e.g., keyboards, pointing devices, displays 24, etc.), may communicate with one or more devices that enable a user to interact with the server 12, and / or may communicate with any device that enables the server 12 to communicate with one or more other computing devices (e.g., network cards, modems, etc.). Such communication may be performed via an input / output (I / O) interface 22. In addition, the server 12 may also communicate with one or more networks (e.g., local area networks (LANs), wide area networks (WANs), and / or public networks, such as the Internet) via a network adapter 20. As shown, the network adapter 20 communicates with other modules of the server 12 via a bus 18. It should be understood that, although not shown in the figure, the server 12 may be assembled to use other hardware and / or software modules, including but not limited to: microcode, device drivers, redundant processing units, external disk drive arrays, RAID servers, tape drives, and data backup storage servers, etc.

[0116] The processing unit 16 executes various functional applications and data processing by running the programs stored in the server memory 28, such as implementing the atom identification and selection method provided in the embodiment of the present invention.

[0117] Embodiment 4

[0118] Embodiment 4 of the present invention further provides a storage medium comprising computer executable instructions, wherein the computer executable instructions, when executed by a computer processor, are used to execute any of the atom identification and selection methods provided in the above embodiments.

[0119] The computer storage medium of the embodiment of the present invention may adopt any combination of one or more computer-readable media. The computer-readable medium may be a computer-readable signal medium or a computer-readable storage medium. The computer-readable storage medium may be, for example, but not limited to, an electrical, magnetic, optical, electromagnetic, infrared, or semiconductor system, device or device, or any combination of the above. More specific examples (a non-exhaustive list) of computer-readable storage media include: an electrical connection with one or more wires, a portable computer disk, 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 this document, a computer-readable storage medium may be any tangible medium containing or storing a program that may be used by or in conjunction with an instruction execution system, device or device.

[0120] Computer-readable signal media may include data signals propagated in baseband or as part of a carrier wave, which carry computer-readable program code. Such propagated data signals may take a variety of forms, including but not limited to electromagnetic signals, optical signals, or any suitable combination of the above. Computer-readable signal media may also be any computer-readable medium other than a computer-readable storage medium, which may send, propagate, or transmit a program for use by or in conjunction with an instruction execution system, apparatus, or device.

[0121] Program code embodied on a computer readable medium may be transmitted using any appropriate medium, including but not limited to wireless, wireline, optical fiber cable, RF, etc., or any suitable combination of the foregoing.

[0122] Computer program code for performing the operations of the present invention may be written in one or more programming languages ​​or a combination thereof, including object-oriented programming languages ​​such as Java, Smalltalk, C++, and conventional procedural programming languages ​​such as "C" or similar programming languages. The program code may be executed entirely on the user's computer, partially on the user's computer, as a separate software package, partially on the user's computer and partially on a remote computer, or entirely on a remote computer or device. In the case of a remote computer, the remote computer may 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 may be connected to an external computer (e.g., through the Internet using an Internet service provider).

[0123] Embodiment 5

[0124] An embodiment of the present invention provides a computer program product, which includes a computer program. The computer program can be stored on a non-transitory computer-readable storage medium. When the computer program is executed by a processor, the computer can execute the atom identification and selection method provided in the above embodiment.

[0125] Note that the above are only preferred embodiments of the present invention and the technical principles used. Those skilled in the art will understand that the present invention is not limited to the specific embodiments described herein, and that various obvious changes, readjustments and substitutions can be made by those skilled in the art without departing from the scope of protection of the present invention. Therefore, although the present invention has been described in more detail through the above embodiments, the present invention is not limited to the above embodiments, and may include more other equivalent embodiments without departing from the concept of the present invention, and the scope of the present invention is determined by the scope of the appended claims.

Claims

1. A method for identifying and selecting atoms, characterized in that: include: Obtaining atomic attribution information and atomic coordinates of all atoms, classifying all atoms according to the atomic attribution information, determining ligand atoms and receptor atoms, and calculating the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms; Obtain the relative atomic mass of the ligand atom, screen the ligand atom according to the relative atomic mass, and determine the candidate ligand atom; The distance from each candidate ligand atom to the ligand centroid is calculated according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, the candidate ligand atom closest to the ligand centroid is selected as the first special atom P1, and the candidate ligand atom farthest from the ligand centroid is selected as the second special atom P2; Screening other candidate ligand atoms according to the first preset screening rule, and selecting the third special atom P3; Obtaining the atomic names of the receptor atoms, screening the receptor atoms according to the atomic names, and determining candidate receptor atoms; The distance between each candidate receptor atom and the ligand centroid is calculated according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and the candidate receptor atom closest to the ligand centroid is selected as the fourth special atom P4; The amino acid where the fourth special atom P4 is located is determined according to the atom attribution information of the fourth special atom P4, and other acceptor atoms in the amino acid are screened according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

2. The atom identification and selection method according to claim 1, characterized in that: The atomic coordinates are obtained by parsing the gro file of the molecular dynamics simulation system, and the atomic attribution information, the relative atomic mass of the ligand atoms and the atomic names of the receptor atoms are all obtained by parsing the top file of the molecular dynamics simulation system.

3. The atom identification and selection method according to claim 1, characterized in that: The step of screening the ligand atoms according to the relative atomic mass to determine the candidate ligand atoms comprises: When the relative atomic mass of a ligand atom is greater than 4, the ligand atom is determined as a candidate ligand atom.

4. The atom identification and selection method according to claim 1, characterized in that: The step of screening other candidate ligand atoms according to the first preset screening rule to select the third special atom P3 includes: Calculate the distance L12 between the first special atom P1 and the second special atom P2; The other candidate ligand atoms are sorted according to the distances from the other candidate ligand atoms to the ligand centroid, and the candidate ligand atoms are substituted into the following formula one by one according to the sorting for verification: 0>(L12*L12+L1X*L1X-L2X*L2X) / (2*L12*L1X) Wherein, L1X is the distance from other candidate ligand atoms to the first special atom P1, and L2X is the distance from other candidate ligand atoms to the second special atom P2; When the first candidate ligand atom that makes the above formula valid appears, the candidate ligand atom is determined as the third special atom P3.

5. The atom identification and selection method according to claim 1, characterized in that: The step of screening the receptor atoms according to the atom names to determine the candidate receptor atoms includes: When the atom name of the acceptor atom is CA, the acceptor atom is determined as a candidate acceptor atom.

6. The atom identification and selection method according to claim 1, characterized in that: The step of screening other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6 comprises: obtaining the acceptor atom ordering in the amino acid; The last atom named C in the acceptor atom sequence is selected as the fifth special atom P5, and the last atom named O in the acceptor atom sequence is selected as the sixth special atom P6.

7. An atom identification and selection device, characterized in that: include: A preprocessing module is used to obtain the atomic attribution information and atomic coordinates of all atoms, classify all atoms according to the atomic attribution information, determine the ligand atoms and the receptor atoms, and calculate the position coordinates of the ligand centroid according to the atomic coordinates of the ligand atoms; The first candidate determination module is used to obtain the relative atomic mass of the ligand atom, screen the ligand atom according to the relative atomic mass, and determine the candidate ligand atom; A first calculation module is used to calculate the distance from each candidate ligand atom to the ligand centroid according to the atomic coordinates of the candidate ligand atom and the position coordinates of the ligand centroid, select the candidate ligand atom closest to the ligand centroid as the first special atom P1, and select the candidate ligand atom farthest from the ligand centroid as the second special atom P2; A first screening module, used to screen other candidate ligand atoms according to a first preset screening rule and select a third special atom P3; The second candidate determination module is used to obtain the atomic names of the receptor atoms, screen the receptor atoms according to the atomic names, and determine the candidate receptor atoms; The second calculation module is used to calculate the distance between each candidate receptor atom and the ligand centroid according to the atomic coordinates of the candidate receptor atom and the position coordinates of the ligand centroid, and select the candidate receptor atom closest to the ligand centroid as the fourth special atom P4; The second screening module is used to determine the amino acid where the fourth special atom P4 is located according to the atom attribution information of the fourth special atom P4, and screen other acceptor atoms in the amino acid according to the second preset screening rule to select the fifth special atom P5 and the sixth special atom P6.

8. A server, characterized in that: include: one or more processors; A storage device for storing one or more programs; When the one or more programs are executed by the one or more processors, the one or more processors implement the atom identification and selection method as described in any one of claims 1 to 6.

9. A storage medium comprising computer executable instructions, wherein the computer executable instructions are used to perform the atom identification and selection method according to any one of claims 1 to 6 when executed by a computer processor.

10. A computer product, comprising a computer program, characterized in that: When the computer program is executed by a processor, the atom identification and selection method according to any one of claims 1 to 6 is implemented.

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