CN114300039A - Bioactive component screening system based on virus structural protein - Google Patents
Bioactive component screening system based on virus structural protein Download PDFInfo
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Abstract
The invention relates to a virus structural protein-based bioactive component screening system. In order to shorten the research and development cycle of new antiviral drugs, reduce the research and development cost and improve the research and development success rate, the invention provides a new virus structural protein-based bioactive component screening system, which comprises: the system comprises a first acquisition unit for acquiring the structure file and information of the bioactive component to be screened, a selection unit for inputting the structure file of the bioactive component to be screened into a corresponding molecular docking module according to the information, a second acquisition unit for acquiring the structure file of the virus structural protein, a matching unit for matching the structure file of the virus structural protein and the structure file of the bioactive component to be screened to the same molecular docking module, a molecular docking unit and a visualization unit. The invention simplifies the screening steps of the bioactive components of the virus structural protein, improves the screening speed and efficiency and has very good practical application value.
Description
Technical Field
The invention relates to the field of computer-aided drug design, in particular to a virus structural protein-based bioactive component screening system, a screening method, a device, a system and a computer-readable storage medium.
Background
The research and development of the antiviral drugs are complex system engineering, the time cost and the research and development cost are extremely high, computer-aided drug design (CADD) is an effective method for improving the research and development efficiency of new drugs, and CADD is integrated with molecular biology and other subjects, so that the research and development period of the new drugs is shortened to a certain extent, the research and development cost is reduced, and the research and development success rate is improved.
However, the traditional screening step of bioactive components of virus structural proteins based on CADD comprises complex structural file processing, different processing of the structural files needs different software, developers need to learn and research the software one by one, and even after the developers are familiar with the software, the dispersed running of the different software can lead to a great deal of time spent on the processing of the structural files, and the project development progress is delayed. In addition, although the molecular docking technology is continuously developed, the principles behind many molecular docking software are different, the adopted methods are different, and have advantages and disadvantages, and the selection of each molecular docking software may be far from the results, and which is more suitable for the owned project becomes a difficult problem for research and development personnel.
Disclosure of Invention
In order to simplify the screening steps of the virus structural protein bioactive components and improve the screening speed and efficiency, the invention provides a novel virus structural protein-based bioactive component screening system, a screening method, equipment, a system and a computer-readable storage medium.
The application discloses a bioactive component screening system based on virus structural protein, including:
the device comprises a first acquisition unit, a second acquisition unit and a display unit, wherein the first acquisition unit is used for acquiring a structure file and information of the bioactive components to be screened, and the information comprises the category and the size of the bioactive components;
the selection unit is used for inputting the structure file of the bioactive component to be screened into a corresponding molecular docking module according to the information, wherein the molecular docking module comprises a protein-protein molecular docking module, a protein-large nucleic acid molecular docking module, a protein-small nucleic acid molecular docking module and a protein-small molecular docking module;
a second obtaining unit for obtaining a structural file of the virus structural protein;
the matching unit is used for matching the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecule docking module;
the molecular docking unit is used for enabling the molecular docking module to recognize the binding sites of the virus structural proteins and the three-dimensional conformation of the bioactive components to be screened, and completing the binding and sequencing of the virus proteins and the bioactive components to be screened;
and the visualization unit is used for obtaining the complex of the virus protein with the top rank and the bioactive component to be screened after combination according to the sorting and carrying out three-dimensional visualization display.
Further, the system further comprises a protein structure prediction unit, the protein structure prediction unit is located before the second obtaining unit, and when the original input file is the nucleic acid sequence or the amino acid sequence of the virus structural protein, the protein structure prediction unit is used for generating the structural file of the virus structural protein from the nucleic acid sequence or the amino acid sequence of the virus structural protein, preferably, the protein structure prediction unit is alphafold software.
The invention aims to provide a method for screening a biological active component based on a virus structural protein, which comprises the following steps:
acquiring a structure file and biological information of a bioactive component to be screened, wherein the biological information comprises the category and the size of the bioactive component;
inputting a structural file of the bioactive component to be screened into a corresponding molecular docking module according to the biological information, wherein the molecular docking module comprises a protein-protein molecular docking module, a protein-large nucleic acid molecular docking module, a protein-small nucleic acid molecular docking module and a protein-small molecular docking module;
acquiring a structural file of virus structural protein;
matching the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecular docking module;
the molecular docking module identifies the binding sites of the virus structural proteins and the three-dimensional conformation of the bioactive components to be screened, and completes the binding and sequencing of the virus proteins and the bioactive components to be screened;
and obtaining a compound formed by combining the virus protein with the front rank with the bioactive component to be screened according to the sorting, and performing three-dimensional visual display.
Further, the categories of the bioactive components include proteins, nucleic acids, small molecules;
optionally, when the bioactive component to be screened is a protein, the structural file of the bioactive component to be screened belongs to a protein-protein molecule docking module; when the bioactive components to be screened are small molecules, inputting the structural files of the bioactive components to be screened into a protein-small molecule docking module; when the bioactive component to be screened is nucleic acid, inputting the structural file of the bioactive component to be screened into a protein-small nucleic acid molecule docking module or a protein-large nucleic acid molecule docking module according to the size of the nucleic acid.
Further, after obtaining a structural file of the virus structural protein, preprocessing the structural file of the virus protein, wherein the preprocessing comprises hydrogenation, charge calculation, water molecule removal, impurity atom removal, conversion of non-standard amino acid into standard amino acid, structural integrity inspection and/or structural repair; preferably, the structural repair comprises linking of a structural protein defect or break;
optionally, the biological information is to preprocess the structure file of the bioactive component to be screened before inputting the structure file of the bioactive component to be screened into the corresponding molecular docking module, where the preprocessing includes hydrogenation, charging, chemical bonding, optimizing hydrogen orientation, checking whether there is atom deletion or side chain deletion.
Further, the molecular docking module is selected from one or more of commercial or free molecular docking programs, preferably, the molecular docking program comprises: ligandFit, Glide, GOLD, MOE Dock, Surflex-Dock, CovDOCK, FlexX, ICM-Pro, AutoDock Vina, LeDock, rDock, UCSF DOCK, Rosetta, ZDCK, GRAMM-X, HADDOCK, PatchDock;
optionally, the protein-protein molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-large nucleic acid molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-small nucleic acid molecule docking module comprises: autodock, Autodock Vina, HADDOCK, and PatchDock; the protein-small molecule docking module comprises: autodock, LeDock, rDock, Glide, GOLD, Surflex-Dock.
Further, the molecular docking module is a combination of more than two molecular docking programs, and the sequence is an average value of scoring results of scoring functions of the molecular docking programs;
preferably, the protein-protein molecular docking module comprises a combination of one or more of Rosetta, ZDOCK, and GRAMM-X; the protein-large nucleic acid molecule docking module comprises: one or more of Rosetta, ZDOK and GRAMM-X; the protein-small nucleic acid molecule docking module comprises: autodock, Autodock Vina, HADDOCK, and PatchDock; the protein-small molecule docking module comprises: autodock, LeDock, rDock, Glide, GOLD, Surflex-Dock.
Further, the three-dimensional visual display is realized through a plug-in capable of reading the PDB file, and preferably, the three-dimensional visual display is realized through software VMD.
The object of the present application is to provide an apparatus for screening biologically active components based on viral structural proteins, said apparatus comprising: a memory and a processor;
the memory is to store program instructions;
the processor is configured to invoke program instructions that, when executed, perform the above-described viral structural protein-based bioactive ingredient screening method.
A computer-readable storage medium on which a computer program is stored, which, when executed by a processor, implements the above-described virus structural protein-based bioactive component screening method.
The application has the advantages that:
1. the method integrates various software units used in the screening process of the bioactive components of the virus structural protein to form a bioactive component screening system based on the virus structural protein, simplifies the screening step of the bioactive components of the virus structural protein, improves the screening speed, and greatly simplifies the operation steps and the operation difficulty of research personnel because an original input file is not limited to the virus structural protein with a structural file but also can be a nucleic acid sequence or an amino acid sequence of the virus structural protein in the screening process of the bioactive components of the virus structural protein;
2. the application adds visualization after molecule docking, screens the docked compound, and realizes visual and effective three-dimensional visualization display to check whether the docking of the protein compound is reasonable. Although the molecular docking software adopts different scoring functions, the scoring functions of the molecular docking software have poor generalization due to the complexity and variability of the molecular docking, and manual rechecking is required;
3. the application innovatively classifies and integrates the molecular docking module software, and the obtained information of the bioactive components to be screened is matched with different types of molecular docking software, so that efficient screening is realized;
4. the application also innovatively integrates the software of each molecular docking module, selects the appropriate type of molecular docking software for matching, integrates the software based on different molecular docking software conformation sampling performance and different principles of scoring functions, and effectively avoids excessive deviation caused by single molecular docking according to the scoring of the scoring functions of each molecular docking software in sequencing.
Drawings
In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the drawings needed to be used in the description of the embodiments will be briefly introduced below, and it is obvious that the drawings in the following description are only some embodiments of the present invention, and it is obvious for those skilled in the art to obtain other drawings based on these drawings without creative efforts.
FIG. 1 is a flow chart of a method for screening a bioactive component based on a virus structural protein according to an embodiment of the present invention;
FIG. 2 is a schematic flow chart of a system for screening bioactive components based on virus structural proteins according to an embodiment of the present invention;
FIG. 3 is a schematic diagram of a device for screening bioactive components based on viral structural proteins according to an embodiment of the present invention;
FIG. 4 is a page display diagram of a virus structural protein-based bioactive component screening system provided in an embodiment of the present invention.
Detailed Description
In order to make the technical solutions of the present invention better understood, the technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention.
In some of the flows described in the present specification and claims and in the above figures, a number of operations are included that occur in a particular order, but it should be clearly understood that these operations may be performed out of order or in parallel as they occur herein, with the order of the operations being indicated as 101, 102, etc. merely to distinguish between the various operations, and the order of the operations by themselves does not represent any order of performance. Additionally, the flows may include more or fewer operations, and the operations may be performed sequentially or in parallel. It should be noted that, the descriptions of "first", "second", etc. in this document are used for distinguishing different messages, devices, modules, etc., and do not represent a sequential order, nor limit the types of "first" and "second" to be different.
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
FIG. 1 is a schematic flow chart of a method for screening a bioactive component based on a virus structural protein, which comprises the following steps:
101: acquiring a structure file and information of a bioactive component to be screened, wherein the information comprises the category and the size of the bioactive component;
in one embodiment, the class of bioactive components includes proteins, nucleic acids, small molecules.
In one embodiment, the nucleic acid includes DNA and RNA, single-stranded, double-stranded, etc., preferably, the size of the nucleic acid is a threshold of 9, 12, 15, 18, 21 nucleotides, smaller than the threshold is a small nucleic acid, and larger than the threshold is a large nucleic acid molecule.
In one embodiment, the structural file of the bioactive component to be screened is preprocessed before being input into the corresponding molecular docking module, and the preprocessing includes hydrogenation, charge calculation, chemical bond optimization, hydrogen orientation optimization, checking whether atoms are absent or not, and whether side chains are absent or not.
In one embodiment, the charge of the small molecule is calculated using different empirical charge calculation methods (e.g., any one or combination of Del-Re, formal, GM, GH, Huckel, MMFF, and Pullman).
102: inputting the structure file of the bioactive component to be screened into a corresponding molecular docking module according to the information, wherein the molecular docking module comprises a protein-protein molecular docking module, a protein-large nucleic acid molecular docking module, a protein-small nucleic acid molecular docking module and a protein-small molecular docking module;
in one embodiment, when the bioactive component to be screened is a protein, the structural file of the bioactive component to be screened belongs to the protein-protein molecule docking module; when the bioactive components to be screened are small molecules, inputting the structural files of the bioactive components to be screened into a protein-small molecule docking module; when the bioactive component to be screened is nucleic acid, inputting the structural file of the bioactive component to be screened into a protein-small nucleic acid molecule docking module or a protein-large nucleic acid molecule docking module according to the size of the nucleic acid.
In one embodiment, the molecular docking module is selected from one or more of commercial or free molecular docking programs, preferably, the molecular docking program comprises: ligandFit, Glide, GOLD, MOE Dock, Surflex-Dock, CovDOCK, FlexX, ICM-Pro, AutoDock Vina, LeDock, rDock, UCSF DOCK, Rosetta, ZDDOK, GRAMM-X, HADDOCK, PatchDock.
In one embodiment, the protein-protein molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-large nucleic acid molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-small nucleic acid molecule docking module comprises: autodock, Autodock Vina, HADDOCK, and PatchDock; the protein-small molecule docking module comprises: autodock, LeDock, rDock, Glide, GOLD, Surflex-Dock.
103: acquiring a structural file of virus structural protein;
in one embodiment, when the original input file is a nucleic acid sequence or an amino acid sequence of a viral structural protein, the nucleic acid sequence or the amino acid sequence of the viral structural protein is used to generate a structural file of the viral structural protein, preferably, the protein structure prediction unit is alphafold or rosettafald software.
In one embodiment, the structural file of the virus structural protein is obtained and then is preprocessed, wherein the preprocessing comprises hydrogenation, charge calculation, water molecule removal, atomic removal, non-standard amino acid conversion into standard amino acid, structural integrity check and/or structural repair; preferably, the structural repair comprises attachment of a structural protein defect or break.
In one embodiment, the charge calculation uses the gastiger method to calculate the charge of the virus structural protein and to perform hydrotreating.
In one embodiment, when the structural file of the structural protein of the virus is obtained from the PDB database, a structural integrity check is performed using a software package such as Sybyl-x.
104: matching the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecular docking module;
105: the molecular docking module identifies the binding sites of the virus structural proteins and the three-dimensional conformation of the bioactive components to be screened, and completes the binding and sequencing of the virus proteins and the bioactive components to be screened;
in one embodiment, the molecular docking module is a combination of two or more molecular docking procedures, and the ranking is an average of scoring results of scoring functions of the respective molecular docking procedures. The core calculation formulas of the molecular docking software in the market are rough, and are roughly divided into four categories, namely a physical-based scoring function, an empirical-based scoring function, a knowledge-based scoring function and a description-based scoring function according to different principles. Various scoring functions have advantages and disadvantages, so a method of averaging the scoring results of the scoring functions of various molecular docking programs can be adopted, or a mode of summing the scoring results of different scoring functions after multiplying the scoring results by the weights of the scoring functions can be adopted to obtain a better result.
In one embodiment, the protein-protein molecular docking module comprises a combination of one or more of Rosetta, ZDOCK, and GRAMM-X, and the ranking is an average of the ranking results of the combined scoring functions of one or more of Rosetta, ZDOCK, and GRAMM-X; the protein-large nucleic acid molecule docking module comprises: the ranking is the average value of the scoring results of the combined scoring functions of one or more of Rosetta, ZDCK and GRAMM-X; the protein-small nucleic acid molecule docking module comprises: the sorting is the averaging of the scoring results of the combined scoring functions of one or more of the Autodock, the Autodock Vina, the HADDOCK and the Patch dock; the protein-small molecule docking module comprises: the sequence is the average value of scoring results of a combined scoring function of one or more of the Autodock, the LeDock, the rDock, the Glide, the GOLD and the Surflex-Dock.
106: and obtaining a compound formed by combining the virus protein with the front rank with the bioactive component to be screened according to the sorting, and performing three-dimensional visual display.
In one embodiment, the three-dimensional visual presentation is implemented by a plug-in that can read the PDB file, and preferably, the three-dimensional visual presentation is implemented by a software VMD.
FIG. 2 is a device for screening bioactive components based on virus structural proteins, according to an embodiment of the present invention, the device comprising: a memory and a processor;
the memory is to store program instructions;
the processor is configured to invoke program instructions that, when executed, perform the above-described viral structural protein-based bioactive ingredient screening method.
FIG. 3 is a system for screening bioactive components based on virus structural proteins, according to an embodiment of the present invention, including:
a first obtaining unit 301, configured to obtain a structure file and information of a bioactive component to be screened, where the information includes a category and a size of the bioactive component;
a selecting unit 302, configured to input a structure file of a bioactive component to be screened into a corresponding molecular docking module according to the information, where the molecular docking module includes a protein-protein molecular docking module, a protein-large nucleic acid molecule docking module, a protein-small nucleic acid molecule docking module, and a protein-small molecule docking module;
a second obtaining unit 303, configured to obtain a structural file of a virus structural protein;
a matching unit 304, configured to match the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecule docking module;
a molecule docking unit 305, configured to recognize the binding site of the virus structural protein and the three-dimensional conformation of the bioactive component to be screened by the molecule docking module, and complete the binding and sequencing between the virus protein and the bioactive component to be screened;
and the visualization unit 306 is used for obtaining the complex of the virus protein with the top rank and the bioactive component to be screened after combination according to the sorting and performing three-dimensional visualization display.
Preferably, the system further comprises a protein structure prediction unit, the protein structure prediction unit is located before the second obtaining unit, and when the original input file is the nucleic acid sequence or the amino acid sequence of the virus structural protein, the protein structure prediction unit is used for generating the structural file of the virus structural protein from the nucleic acid sequence or the amino acid sequence of the virus structural protein, and preferably, the protein structure prediction unit is alphafold or rosettafald software.
Preferably, the system further comprises a pretreatment unit, wherein the pretreatment protein is used for pretreating the acquired structure file, and the pretreatment comprises hydrogenation, charge calculation, water molecule removal, atomic removal, non-standard amino acid conversion to standard amino acid, structural integrity check and/or structural repair of the protein structure file; the pretreatment also comprises the steps of hydrogenation, charge addition, chemical bond optimization, hydrogen orientation optimization, and checking whether atomic deletion and/or side chain deletion exist/exist on the small molecular structure file. Preferably, the pretreatment unit is
In one embodiment, the first acquisition unit and the second acquisition unit of the system are structured and sequence files, and the supported protein and nucleic acid macromolecule files comprise: PDB structure file format, fasta sequence format; the small molecule file comprises: sdf, pdb, pdbqt structural formula documents. The system can automatically judge and process the uploaded files, and if the sequence data is uploaded, the system automatically carries out protein structure prediction through a protein structure prediction unit. And automatically carrying out conventional data processing such as hydrogenation, charge calculation and the like on the structure file.
In one embodiment, the page of the virus structural protein-based bioactive component screening system is displayed as shown in fig. 4, in a web page, a virus structural protein (Receptor), a bioactive component structural file of the virus structural protein, wherein the structural file can be a structural file after pretreatment, and the bioactive component of the virus structural protein can be a protein, a nucleic acid or a small molecule; and clicking Submit, performing molecular docking on the virus structural protein and the bioactive components of the virus structural protein, and displaying on a front-end webpage after the operation is finished.
A computer-readable storage medium, on which a computer program is stored, which, when being executed by a processor, implements the above-mentioned virus structural protein-based bioactive component screening method.
The validation results of this validation example show that assigning an intrinsic weight to an indication can moderately improve the performance of the method relative to the default settings.
It is clear to those skilled in the art that, for convenience and brevity of description, the specific working processes of the above-described systems, apparatuses and units may refer to the corresponding processes in the foregoing method embodiments, and are not described herein again.
In the several embodiments provided in the present application, it should be understood that the disclosed system, apparatus and method may be implemented in other manners. For example, the above-described apparatus embodiments are merely illustrative, and for example, the division of the units is only one logical division, and other divisions may be realized in practice, for example, a plurality of units or components may be combined or integrated into another system, or some features may be omitted, or not executed. In addition, the shown or discussed mutual coupling or direct coupling or communication connection may be an indirect coupling or communication connection through some interfaces, devices or units, and may be in an electrical, mechanical or other form.
The units described as separate parts may or may not be physically separate, and parts displayed as units may or may not be physical units, may be located in one place, or may be distributed on a plurality of network units. Some or all of the units can be selected according to actual needs to achieve the purpose of the solution of the embodiment.
In addition, functional units in the embodiments of the present invention may be integrated into one processing unit, or each unit may exist alone physically, or two or more units are integrated into one unit. The integrated unit can be realized in a form of hardware, and can also be realized in a form of a software functional unit.
Those skilled in the art will appreciate that all or part of the steps in the methods of the above embodiments may be implemented by associated hardware instructed by a program, which may be stored in a computer-readable storage medium, and the storage medium may include: read Only Memory (ROM), Random Access Memory (RAM), magnetic or optical disks, and the like.
It will be understood by those skilled in the art that all or part of the steps in the method for implementing the above embodiments may be implemented by hardware that is instructed to implement by a program, and the program may be stored in a computer-readable storage medium, and the above-mentioned storage medium may be a read-only memory, a magnetic disk or an optical disk, etc.
While the invention has been described in detail with reference to specific embodiments thereof, it will be apparent to one skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention.
Claims (10)
1. A virus structural protein-based bioactive component screening system comprising:
the device comprises a first acquisition unit, a second acquisition unit and a display unit, wherein the first acquisition unit is used for acquiring a structure file and information of the bioactive components to be screened, and the information comprises the category and the size of the bioactive components;
the selection unit is used for inputting the structure file of the bioactive component to be screened into a corresponding molecular docking module according to the information, wherein the molecular docking module comprises a protein-protein molecular docking module, a protein-large nucleic acid molecular docking module, a protein-small nucleic acid molecular docking module and a protein-small molecular docking module;
a second obtaining unit for obtaining a structural file of the virus structural protein;
the matching unit is used for matching the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecule docking module;
the molecular docking unit is used for enabling the molecular docking module to recognize the binding sites of the virus structural proteins and the three-dimensional conformation of the bioactive components to be screened, and completing the binding and sequencing of the virus proteins and the bioactive components to be screened;
and the visualization unit is used for obtaining the complex of the virus protein with the top rank and the bioactive component to be screened after combination according to the sorting and carrying out three-dimensional visualization display.
2. The system for screening bioactive components based on virus structural proteins according to claim 1, further comprising a protein structure prediction unit, wherein the protein structure prediction unit is located before the second obtaining unit, and when the original input file is the nucleic acid sequence or amino acid sequence of the virus structural protein, the protein structure prediction unit is used for generating the structural file of the virus structural protein from the nucleic acid sequence or amino acid sequence of the virus structural protein, preferably, the protein structure prediction unit is alphafold or rosettafald software.
3. A method for screening a bioactive component based on a virus structural protein, comprising:
acquiring a structure file and information of a bioactive component to be screened, wherein the information comprises the category and the size of the bioactive component;
inputting the structure file of the bioactive component to be screened into a corresponding molecular docking module according to the information, wherein the molecular docking module comprises a protein-protein molecular docking module, a protein-large nucleic acid molecular docking module, a protein-small nucleic acid molecular docking module and a protein-small molecular docking module;
acquiring a structural file of virus structural protein;
matching the structural file of the virus structural protein and the structural file of the bioactive component to be screened to the same molecular docking module;
the molecular docking module identifies the binding sites of the virus structural proteins and the three-dimensional conformation of the bioactive components to be screened, and completes the binding and sequencing of the virus proteins and the bioactive components to be screened;
and obtaining a compound formed by combining the virus protein with the front rank with the bioactive component to be screened according to the sorting, and performing three-dimensional visual display.
4. The method of claim 1, wherein the bioactive component is selected from the group consisting of proteins, nucleic acids, small molecules;
optionally, when the bioactive component to be screened is a protein, the structural file of the bioactive component to be screened belongs to a protein-protein molecule docking module; when the bioactive components to be screened are small molecules, inputting the structural files of the bioactive components to be screened into a protein-small molecule docking module; when the bioactive component to be screened is nucleic acid, inputting the structural file of the bioactive component to be screened into a protein-small nucleic acid molecule docking module or a protein-large nucleic acid molecule docking module according to the size of the nucleic acid.
5. The method of claim 1, wherein the structural file of the viral protein is obtained and then pre-treated, and the pre-treatment comprises hydrogenation, charge calculation, water molecule removal, atom removal, conversion of non-standard amino acids to standard amino acids, structural integrity check and/or structural repair; preferably, the structural repair comprises linking of a structural protein defect or break;
optionally, the structural file of the bioactive component to be screened is preprocessed before being input into the corresponding molecular docking module, where the preprocessing includes hydrogenation, charging, chemical bonding, optimizing hydrogen orientation, checking whether there is atom deletion or side chain deletion.
6. The method for screening bioactive components based on virus structural proteins of claim 1, wherein the molecular docking module is selected from one or more of commercial or free molecular docking programs, preferably the molecular docking program comprises: ligandFit, Glide, GOLD, MOE Dock, Surflex-Dock, CovDOCK, FlexX, ICM-Pro, AutoDock Vina, LeDock, rDock, UCSF DOCK, Rosetta, ZDCK, GRAMM-X, HADDOCK, PatchDock;
optionally, the protein-protein molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-large nucleic acid molecule docking module comprises: rosetta, ZDOT, GRAMM-X; the protein-small nucleic acid molecule docking module comprises: autodock, Autodock Vina, HADDOCK, and PatchDock; the protein-small molecule docking module comprises: autodock, LeDock, rDock, Glide, GOLD, Surflex-Dock.
7. The method of claim 1, wherein the molecular docking module is a combination of two or more molecular docking programs, and the ranking is an average of scoring results of scoring functions of the respective molecular docking programs;
preferably, the protein-protein molecular docking module comprises a combination of one or more of Rosetta, ZDOCK, and GRAMM-X; the protein-large nucleic acid molecule docking module comprises: one or more of Rosetta, ZDOK and GRAMM-X; the protein-small nucleic acid molecule docking module comprises: autodock, Autodock Vina, HADDOCK, and PatchDock; the protein-small molecule docking module comprises: autodock, LeDock, rDock, Glide, GOLD, Surflex-Dock.
8. The method for screening bioactive components based on viral structural proteins according to claim 1, characterized in that said three-dimensional visualization is realized by means of an insert that can read the PDB file, preferably by means of software VMD.
9. An apparatus for screening biologically active components based on viral structural proteins, said apparatus comprising: a memory and a processor;
the memory is to store program instructions;
the processor is configured to invoke program instructions for performing the method of any one of claims 3 to 7 for screening a viral structural protein-based bioactive ingredient.
10. A computer-readable storage medium on which a computer program is stored, the computer program, when being executed by a processor, implementing the method for screening a viral structural protein-based bioactive component according to any of the preceding claims 3 to 7.
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| Publication number | Priority date | Publication date | Assignee | Title |
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| CN115295091A (en) * | 2022-08-08 | 2022-11-04 | 苏州创腾软件有限公司 | Molecular docking method and system based on AutoDock visual platform |
| CN115862768A (en) * | 2022-12-11 | 2023-03-28 | 南昌大学 | Optimization method for large-scale virtual drug screening |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| CN115295091A (en) * | 2022-08-08 | 2022-11-04 | 苏州创腾软件有限公司 | Molecular docking method and system based on AutoDock visual platform |
| CN115295091B (en) * | 2022-08-08 | 2023-09-01 | 苏州创腾软件有限公司 | Molecular docking method and system based on AutoDock visual platform |
| CN115862768A (en) * | 2022-12-11 | 2023-03-28 | 南昌大学 | Optimization method for large-scale virtual drug screening |
| CN115862768B (en) * | 2022-12-11 | 2023-09-01 | 南昌大学 | Optimization method for large-scale drug virtual screening |
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