CN115295091A - Molecular docking method and system based on AutoDock visual platform - Google Patents
Molecular docking method and system based on AutoDock visual platform Download PDFInfo
- Publication number
- CN115295091A CN115295091A CN202210947895.4A CN202210947895A CN115295091A CN 115295091 A CN115295091 A CN 115295091A CN 202210947895 A CN202210947895 A CN 202210947895A CN 115295091 A CN115295091 A CN 115295091A
- Authority
- CN
- China
- Prior art keywords
- ligand
- docking
- information
- molecular docking
- receptor
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
Images
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/50—Molecular design, e.g. of drugs
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/80—Data visualisation
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
Landscapes
- Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Chemical & Material Sciences (AREA)
- Computing Systems (AREA)
- Crystallography & Structural Chemistry (AREA)
- Life Sciences & Earth Sciences (AREA)
- Bioinformatics & Computational Biology (AREA)
- Theoretical Computer Science (AREA)
- Health & Medical Sciences (AREA)
- General Health & Medical Sciences (AREA)
- Medicinal Chemistry (AREA)
- Pharmacology & Pharmacy (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Physics & Mathematics (AREA)
- Data Mining & Analysis (AREA)
- Investigating Or Analysing Biological Materials (AREA)
Abstract
The embodiment of the invention discloses a molecular docking method and a system based on an AutoDock visual platform, wherein the method comprises the following steps: obtaining structural information of a ligand molecule and structural information of a receptor molecule; generating ligand input information in a preset format according to the structural information of the ligand molecules, and generating receptor input information in a preset format according to the structural information of the receptor molecules; generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters; and generating an output file according to each molecular docking result, and outputting the output file so as to display the output file at the front end of the visual platform. The problem of the prior art that when a visual platform is used for molecular docking, a command line script needs to be called manually, and therefore operation difficulty is large is solved.
Description
Technical Field
The invention relates to the technical field of artificial intelligence, in particular to a molecular docking method and a molecular docking system based on an AutoDock visual platform.
Background
In the field of drug development, small molecule compounds with biological activity can interact with specific protein targets to influence the biological functions of the protein and related proteins, thereby regulating and controlling the life activities of organisms or generating therapeutic effects on diseases.
Molecular docking is a common technology in the development of small molecule drugs, is used for researching an interaction mode between a small molecule and a macromolecule (namely protein) in a computer, evaluating the strength of interaction and the like, and provides theoretical support for optimization of a lead compound. In the molecular docking process, small molecules are often referred to as ligands and large proteins as receptors.
In the related technology, an open-source visualization platform Autodock can be used for molecular docking, but the platform does not support a graphical interface, an input file of the platform needs to be in a special format (PDBQT file), and in the process of preparing the input file, a user needs to call a command line script depending on professional knowledge in the pharmaceutical field and the computer field, so that the human-computer interaction friendliness is poor, and the operation difficulty is high; moreover, the result file output by the existing platform is inconvenient to check, and the interaction possibly existing between the ligand and the receptor cannot be analyzed, so that the visibility of the molecular docking result is poor.
Disclosure of Invention
Therefore, the embodiment of the invention provides a molecular docking method and a molecular docking system based on an AutoDock visual platform, so as to at least partially solve the problem of great operation difficulty caused by manually calling a command line script when a visual platform is adopted for molecular docking in the prior art.
In order to achieve the above object, the embodiments of the present invention provide the following technical solutions:
a molecular docking method based on an AutoDock visual platform is applied to the back end of the visual platform, and comprises the following steps:
obtaining structural information of ligand molecules and structural information of receptor molecules;
generating ligand input information in a preset format according to the structural information of the ligand molecules, and generating receptor input information in a preset format according to the structural information of the receptor molecules;
generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters;
and generating an output file according to each molecular docking result, and outputting the output file so as to display the output file at the front end of the visual platform.
In some embodiments, generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters further comprises:
judging the state of the molecular docking result based on a preset judgment rule;
processing the molecular docking result according to the state of the molecular docking result, and generating the output file based on the processed molecular docking result;
wherein the state of the molecular docking result comprises docking success or docking failure.
In some embodiments, processing the molecule docking result according to the state of the molecule docking result, and generating the output file based on the processed molecule docking result specifically includes:
if the molecular docking result is judged to be successfully docked, calculating the molecular parameters of the ligand molecules to obtain ligand parameter information, and reconstructing the chemical bonds of the ligand molecules;
and combining the ligand parameter information, the ligand molecules after chemical bond reconstruction and the receptor molecules to serve as the molecular docking result, and forming an output file.
In some embodiments, the ligand parameter information comprises at least one of:
the ligand molecule has molecular weight, molecular formula, ring number, hydrogen bond donor number, hydrogen bond acceptor number, logP property, TPSA property and Lipinski property.
In some embodiments, if it is determined that the state of the molecular docking result is a docking failure, the ligand input information and the receptor input information are used as molecular docking results, and an output file is formed.
The invention also provides a molecular docking method based on the AutoDock visual platform, which is applied to the front end of the visual platform and comprises the following steps:
acquiring an output file, and displaying the output file in an image form;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structure information of ligand molecules; the receptor input information is information in a preset format generated according to structural information of receptor molecules.
The invention also provides a molecular docking system based on the AutoDock visual platform, which is applied to the back end of the visual platform, and the system comprises:
an information acquisition unit for acquiring structural information of the ligand molecule and structural information of the receptor molecule;
the input file generating unit is used for generating ligand input information in a preset format according to the structural information of the ligand molecules and generating receptor input information in a preset format according to the structural information of the receptor molecules;
a docking result generation unit for generating at least one molecular docking result based on the ligand input information, the receptor input information and the docking parameters in response to the inputted docking parameters;
and the file output unit is used for generating an output file according to each molecular docking result and outputting the output file so as to display the output file at the front end of the visual platform.
The invention also provides a molecular docking system based on the AutoDock visual platform, which is applied to the front end of the visual platform, and the system comprises:
the output file display unit is used for acquiring an output file and displaying the output file in an image form;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structure information of ligand molecules; the receptor input information is information in a preset format generated based on structural information of the receptor molecule.
The invention also provides an electronic device comprising a memory, a processor and a computer program stored on the memory and executable on the processor, the processor implementing the steps of the method as described above when executing the program.
The invention also provides a non-transitory computer readable storage medium having stored thereon a computer program which, when executed by a processor, implements the steps of the method as described above.
According to the molecular docking method based on the AutoDock visual platform, the structural information of ligand molecules and the structural information of receptor molecules are obtained, ligand input information in a preset format is generated according to the structural information of the ligand molecules, and receptor input information in the preset format is generated according to the structural information of the receptor molecules; generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters; and generating an output file according to each molecular docking result, and outputting the output file so as to display the output file at the front end of the visual platform.
In the using process, the recognizable input information can be generated only by inputting the file containing the structural information of the ligand molecules and the receptor molecules, and the output file containing the molecular docking result is generated and displayed according to the input docking parameters and the input information, so that a command line script is not required to be called, the requirement on the professional ability of an operator is lowered, and the operation difficulty is lowered. Therefore, the problem that operation difficulty is high due to the fact that a command line script needs to be called manually when a visual platform is adopted for molecular docking in the prior art is solved.
Drawings
In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below. It should be apparent that the drawings in the following description are merely exemplary, and that other embodiments can be derived from the drawings provided by those of ordinary skill in the art without inventive effort.
The structures, ratios, sizes, and the like shown in the present specification are only used for matching with the contents disclosed in the specification, so as to be understood and read by those skilled in the art, and are not used to limit the conditions that the present invention can be implemented, so that the present invention has no technical significance, and any structural modifications, changes in the ratio relationship, or adjustments of the sizes, without affecting the effects and the achievable by the present invention, should still fall within the range that the technical contents disclosed in the present invention can cover.
FIG. 1 is a flow chart of a molecular docking method based on an AutoDock visual platform according to the present invention;
FIG. 2 is a second flowchart of the molecular docking method based on the AutoDock visual platform provided in the present invention;
FIG. 3 is a third flowchart of the molecular docking method based on the AutoDock visual platform provided in the present invention;
FIG. 4 is a fourth flowchart of the molecular docking method based on the AutoDock visual platform provided in the present invention;
FIG. 5 is a structural block diagram of a molecular docking system based on an AutoDock visualization platform according to the present invention;
fig. 6 is a second structural block diagram of the molecular docking system based on the AutoDock visualization platform according to the present invention;
fig. 7 is a block diagram of a computer device according to the present invention.
Detailed Description
The present invention is described in terms of particular embodiments, other advantages and features of the invention will become apparent to those skilled in the art from the following disclosure, and it is to be understood that the described embodiments are merely exemplary of the invention and that it is not intended to limit the invention to the particular embodiments disclosed. 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.
In order to solve the problem that the operation difficulty is large due to the fact that a command line script needs to be called manually when a visual platform is adopted for molecular docking in the prior art, so that the learning cost of software is reduced, and the molecular docking technology can better serve drug research and development, the invention provides a molecular docking method based on an Autodock visual platform, which is based on the Autodock and is added with an intelligent and automatic processing flow, and the method converts structure files in various formats uploaded by a user into a PDBQT format special for the Autodock Vina by automatically processing input files; automatically judging the geometric information of the original ligand in the macromolecule, and using the information for molecular docking; the macromolecular structure is automatically pretreated, so that the macromolecular structure can be directly used for molecular docking; the output results of the molecular docking are automatically analyzed, so that a user can conveniently check the conformation of each molecule and the potential receptor-ligand interaction, thereby opening up all links of the molecular docking and providing a one-stop solution of the molecular docking.
Referring to fig. 1, fig. 1 is a flowchart of a molecular docking method based on an AutoDock visualization platform according to the present invention.
In a specific embodiment, the molecular docking method based on the AutoDock visualization platform provided by the invention is applied to the back end of the visualization platform, and the method comprises the following steps:
s101: structural information of the ligand molecule and structural information of the receptor molecule are obtained. In a specific use scenario, the user interface is implemented based on a web, provides an upload button to a user, and supports storage formats of various common chemical structures including PDB and MOL. The user uploads an original file to be used to the server without any conversion operation in advance, and the original file contains the structural information of the ligand molecules and the structural information of the receptor molecules.
S102: and generating ligand input information in a preset format according to the structural information of the ligand molecules, and generating receptor input information in a preset format according to the structural information of the receptor molecules, wherein the preset format is a PDBQT format recognizable by the Autodock. After the structural information of the ligand molecules is obtained, an Autodock Tools plug-in a visual platform can be directly called to convert the Autodock Tools plug-in into a PDBQT format, so that ligand input information is generated. For receptor molecules (i.e. macromolecular proteins), after acquiring the structural information, the receptor molecules need to be preprocessed, converted into the PDBQT format, and used as receptor input information.
Specifically, the proteins used for molecular docking often need to be processed to enter the docking step, for example, original ligands and water molecules in the proteins need to be removed, in this embodiment, automatic processing of non-amino acid residues in the structure is realized by removing atoms marked by the hettm field in the PDB file, so as to obtain a receptor file completely composed of amino acids, and then hydrogenation and charging operations are performed by calling Autodock Tools for the proteins, and the processed proteins are stored in the PDBQT format, so as to generate receptor input information for the subsequent docking step.
S103: generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters. In the actual use process, if a plurality of small molecules (namely ligands) are uploaded by a user, each small molecule and a macromolecule (namely a receptor) are docked circularly, a molecule docking result is generated after each docking, the plurality of small molecules can obtain a plurality of molecule docking results, and if the plurality of macromolecules are uploaded, the first macromolecule read by a program is used as the receptor.
S104: and generating an output file according to each molecular docking result, and outputting the output file so as to display the output file at the front end of the visual platform.
Specifically, after corresponding receptor and ligand files are processed, an Autodock Vina program is called in the background, and the files and parameters are input into the Autodock Vina program, so that an original output file of the Autodock Vina is obtained. The original output file is the conformation of the small molecule ligand, wherein no inter-atom bonding information exists, the bonding information stored in the input file uploaded by a user is read, the corresponding relation of atoms between the input file and the output file is established through atom coordinates, chemical bonds are added to the atoms in the output file, the small molecule ligand and protein are combined into a PDB file, different small molecule conformations are distinguished by MODEL fields in the PDB file, and the whole file is transmitted back to the front end.
Furthermore, before molecular docking, a search area can be obtained, and by locking the search area, the processing quantity of data is reduced, and the data processing efficiency is improved. After a user uploads a file (PDB format) storing protein, a background analyzes the file, extracts all atoms marked as HETATM by traversing all atom records in the file, records the residue names and numbers of the atoms, and transmits the information serving as potential ligand information back to a web interface. After a user selects a certain ligand according to actual needs of the user, the software sends a request to the server again, the server analyzes boundary information (namely xmin, xmax, ymin, ymax, zmin and zmax) of the ligand according to Cartesian coordinates of all atoms in residues in a PDB file according to the name of the ligand selected by the user, converts the boundary information into Cartesian coordinates of a central point and the geometric dimension of the ligand, transmits the converted information to a web interface, and uses the converted information as receptor input information for subsequent docking operation.
In some embodiments, as shown in fig. 2, generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters further comprises:
s201: judging the state of the molecular docking result based on a preset judgment rule; wherein the state of the molecular docking result comprises docking success or docking failure. If Autodock Vina does not find any one of the possible conformations, or if the binding energy of the first ranked conformation is positive, docking failure is indicated, otherwise docking success is indicated.
S202: and processing the molecular docking result according to the state of the molecular docking result, and generating the output file based on the processed molecular docking result. That is to say, when the docking success or the docking failure is the result of the molecular docking, the subsequent steps taken are different, so that the accuracy of the result output is further improved, and after the docking failure, no other calculation operation is needed, so that the calculation amount of the system is reduced.
Specifically, if the molecular docking result is determined to be successfully docked, calculating the molecular parameters of the ligand molecules, such as the molecular weight, molecular formula, ring number, hydrogen bond donor number, hydrogen bond acceptor number, logP property, TPSA property, and Lipinski property of the ligand molecules, to obtain ligand parameter information, and reconstructing the chemical bonds of the ligand molecules;
and combining the ligand parameter information, the ligand molecules after chemical bond reconstruction and the receptor molecules to be used as the molecular docking result, and forming an output file.
And judging that the state of the molecular docking result is a docking failure, taking the ligand input information and the receptor input information as the molecular docking result, and forming an output file.
In order to improve the display effect of the output file and improve the display intuitiveness and visibility, as shown in fig. 3, the invention also provides a molecular docking method based on an AutoDock visual platform, which is applied to the front end of the visual platform, and the method comprises the following steps:
s301: acquiring an output file, and displaying the output file in an image form;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structure information of ligand molecules; the receptor input information is information in a preset format generated according to structural information of receptor molecules.
Specifically, the conventional application method of Autodock Vina can only obtain the conformation of the small molecule after docking, and the interaction between the small molecule and the ligand cannot be observed. According to the invention, by integrating the molecule display engine mol, the molecule structure returned from the rear end is directly displayed on the web page, and a user can switch different small molecule conformations through a mouse. After the small molecule structure displayed in mol is clicked by the left key, the program can focus and display the small molecule, and automatically analyze the potential interaction between the small molecule and the protein, including hydrogen bond, hydrophobic interaction, pi-pi interaction, salt bridge and the like, so that a user can conveniently evaluate the binding capacity between the butted small molecule and the protein.
As shown in fig. 4, a specific usage scenario is taken as an example below to briefly describe an operation process of the molecular docking method based on the AutoDock visualization platform provided by the present invention.
1. The user uploads the small molecules and the large molecules, and the program analyzes the names of the non-standard residues contained in the large molecule file for the user to select. After the user clicks on the residue name, the program automatically analyzes the position and size of the residue and automatically fills the corresponding input box.
2. And clicking a submission button by the user, and submitting the task to the background for calculation. The background program can traverse all the input files, and automatically judge whether the current molecule is a macromolecule or a micromolecule according to the molecular weight, wherein the threshold value of the molecular weight is 3000. When the macromolecule is judged, calling Autodock Tools to carry out macromolecule pretreatment, carrying out operations of hydrogenation, charge addition and nonstandard residue removal, and storing the pretreated macromolecules as a PDBQT format; otherwise, if the structure is judged to be a small molecule, the Autodock Tools are called to directly convert the structure into a PDBQT format. Preparing macromolecules and micromolecules for butt joint, calling an Autodock Vina program, inputting the structure file and butt joint parameters, and carrying out butt joint calculation. If the user uploads a plurality of small molecules, each small molecule is in butt joint with the large molecule in a circulating mode; if multiple macromolecules are uploaded, the first macromolecule read by the program is used as the receptor.
3. If the Autodock Vina does not find any possible conformation, or the binding energy of the first ranked conformation is a positive value, the molecule is judged to have butt joint failure, and the molecule is counted into a failure set without any treatment; otherwise, recording the successful set, calculating the molecular weight, molecular formula, ring number, hydrogen bond donor number, hydrogen bond acceptor number, logP, TPSA and Lipinski properties of the molecule, reconstructing the chemical bond of the molecule, and combining the chemical bond with the acceptor into a file.
4. And transmitting the butted structure to a user, and checking the 3D combination mode and the 2D interaction diagram of the macromolecules and the micromolecules by clicking the record of a certain molecule by the user.
In addition to the above method, the present invention further provides a molecular docking system based on an AutoDock visualization platform, which is applied to a back end of the visualization platform, as shown in fig. 5, and the system includes:
an information acquisition unit 501 for acquiring structural information of a ligand molecule and structural information of a receptor molecule;
an input file generating unit 502, configured to generate ligand input information in a preset format according to the structure information of the ligand molecule, and generate receptor input information in a preset format according to the structure information of the receptor molecule;
a docking result generating unit 503 for generating at least one molecular docking result based on the ligand input information, the receptor input information and the docking parameters in response to the inputted docking parameters;
a file output unit 504, configured to generate an output file from each molecular docking result, and output the output file, so that the front end of the visualization platform displays the output file.
In some embodiments, generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters further comprises:
judging the state of the molecular docking result based on a preset judgment rule;
processing the molecular docking result according to the state of the molecular docking result, and generating the output file based on the processed molecular docking result;
wherein the state of the molecular docking result comprises docking success or docking failure.
In some embodiments, processing the molecule docking result according to the state of the molecule docking result, and generating the output file based on the processed molecule docking result specifically includes:
if the molecular docking result is judged to be successfully docked, calculating the molecular parameters of the ligand molecules to obtain ligand parameter information, and reconstructing the chemical bonds of the ligand molecules;
and combining the ligand parameter information, the ligand molecules after chemical bond reconstruction and the receptor molecules to be used as the molecular docking result, and forming an output file.
In some embodiments, the ligand parameter information comprises at least one of:
the ligand molecule has molecular weight, molecular formula, ring number, hydrogen bond donor number, hydrogen bond acceptor number, logP property, TPSA property and Lipinski property.
In some embodiments, if it is determined that the state of the molecular docking result is a docking failure, the ligand input information and the receptor input information are used as molecular docking results, and an output file is formed.
The invention also provides a molecular docking system based on the AutoDock visualization platform, which is applied to the front end of the visualization platform, as shown in fig. 6, the system comprises:
an output file display unit 601 for acquiring an output file and displaying the output file in the form of an image;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structural information of ligand molecules; the receptor input information is information in a preset format generated based on structural information of the receptor molecule.
In the above embodiments, the molecular docking method and system based on the AutoDock visualization platform provided by the present invention include the following technical effects:
in the using process, the recognizable input information can be generated only by inputting the file containing the structural information of the ligand molecules and the receptor molecules, and the output file containing the molecular docking result is generated and displayed according to the input docking parameters and the input information, so that a command line script is not required to be called, the requirement on the professional ability of an operator is lowered, and the operation difficulty is lowered. Therefore, the problem that operation difficulty is high due to the fact that a command line script needs to be called manually when a visual platform is adopted for molecular docking in the prior art is solved.
According to the technical scheme, complex operations required by a user are automatically processed, a simple operation mode is provided for the user in a visual mode through a web interface, and the user can work in a mode (such as mouse operation) conforming to the conventional software use habit without learning a complex command line operation mode.
The technical scheme provides a method for quickly selecting a search area. Usually, the protein file available to the user contains a small molecule ligand bound to the active region, and in the past, the user needs to manually search for specific parameters (such as center coordinates and volume) of the search region through other visualization software, and in the system, the parameters can be quickly determined by the name of the small molecule ligand and automatically applied in the subsequent steps.
The original file output by the molecular docking program Autodock Vina does not contain chemical bond information of the micromolecule ligand, and the technical scheme adds chemical bonds to the micromolecules in the output file by analyzing the original information in the file uploaded by a user, so that the consistency of the chemical bonds and the input of the user is ensured, and the problem possibly brought by automatic chemical bond presumption is avoided.
The operation of a user is simplified, the use and learning cost of software is reduced, the molecular docking technology can be widely applied, and meanwhile, the user can concentrate on the design of the molecule without paying attention to the operation and data processing of the software.
According to the invention, through a highly automated working process, large-scale virtual screening is easier to perform, a user only needs to provide an original file, and other work can be completed by the system.
The interaction between the ligand and the receptor can be displayed for the user in the form of a two-dimensional image and a three-dimensional image, so that the analysis work is clear at a glance, and the user can further optimize the work of the user.
The method provides a user with a property analysis tool of the small molecule ligand, and provides more useful reference information for the user so as to optimize the small molecule.
In one embodiment, a computer device is provided, which may be a server, the internal structure of which may be as shown in fig. 7. The computer device includes a processor, a memory, and a network interface connected by a system bus. Wherein the processor of the computer device is configured to provide computing and control capabilities. The memory of the computer device comprises a nonvolatile storage medium and an internal memory. The non-volatile storage medium stores an operating system, a computer program, and a model prediction. The internal memory provides an environment for the operation of an operating system and computer programs in the non-volatile storage medium. The model prediction of the computer device is used to store static information and dynamic information data. The network interface of the computer device is used for communicating with an external terminal through a network connection. Which computer program is executed by a processor to carry out the steps of the above-described method embodiments.
Those skilled in the art will appreciate that the architecture shown in fig. 7 is merely a block diagram of some of the structures associated with the inventive arrangements and is not intended to limit the computing devices to which the inventive arrangements may be applied, as a particular computing device may include more or less components than those shown, or may combine certain components, or have a different arrangement of components.
In correspondence with the above embodiments, embodiments of the present invention also provide a computer storage medium containing one or more program instructions. Wherein the one or more program instructions are for performing the method described above by a weight verification system.
The invention also provides a computer program product comprising a computer program, storable on a non-transitory computer readable storage medium, which, when executed by a processor, is capable of executing the above method by a computer.
In an embodiment of the invention, the processor may be an integrated circuit chip having signal processing capability. The Processor may be a general purpose Processor, a Digital Signal Processor (DSP), an Application Specific Integrated Circuit (ASIC), a Field Programmable Gate Array (FPGA) or other programmable logic device, discrete Gate or transistor logic device, discrete hardware component.
The various methods, steps, and logic blocks disclosed in the embodiments of the present invention may be implemented or performed. A general purpose processor may be a microprocessor or the processor may be any conventional processor or the like. The steps of the method disclosed in connection with the embodiments of the present invention may be directly implemented by a hardware decoding processor, or implemented by a combination of hardware and software modules in the decoding processor. The software module may be located in ram, flash memory, rom, prom, or eprom, registers, etc. storage media as is well known in the art. The processor reads the information in the storage medium and completes the steps of the method in combination with the hardware.
The storage medium may be a memory, for example, which may be volatile memory or nonvolatile memory, or which may include both volatile and nonvolatile memory.
The nonvolatile Memory may be a Read-Only Memory (ROM), a Programmable ROM (PROM), an Erasable PROM (EPROM), an Electrically Erasable PROM (EEPROM), or a flash Memory.
The volatile Memory may be a Random Access Memory (RAM) which serves as an external cache. By way of example, and not limitation, many forms of RAM are available, such as Static Random Access Memory (SRAM), dynamic RAM (DRAM), synchronous DRAM (SDRAM), double Data Rate SDRAM (DDRSDRAM), enhanced SDRAM (ESDRAM), SLDRAM (SLDRAM), and Direct Rambus RAM (DRRAM).
The storage media described in connection with the embodiments of the invention are intended to comprise, without being limited to, these and any other suitable types of memory.
Those skilled in the art will appreciate that the functionality described in the present invention may be implemented in a combination of hardware and software in one or more of the examples described above. When software is applied, the corresponding functionality may be stored on or transmitted over as one or more instructions or code on a computer-readable medium. Computer-readable media includes both computer storage media and communication media including any medium that facilitates transfer of a computer program from one place to another. A storage media may be any available media that can be accessed by a general purpose or special purpose computer.
The above embodiments are only for illustrating the embodiments of the present invention and are not to be construed as limiting the scope of the present invention, and any modifications, equivalent substitutions, improvements and the like made on the basis of the embodiments of the present invention shall be included in the scope of the present invention.
Claims (10)
1. A molecular docking method based on an AutoDock visual platform is applied to the back end of the visual platform, and is characterized by comprising the following steps:
obtaining structural information of ligand molecules and structural information of receptor molecules;
generating ligand input information in a preset format according to the structural information of the ligand molecules, and generating receptor input information in a preset format according to the structural information of the receptor molecules;
generating at least one molecular docking result based on the ligand input information, the receptor input information, and the docking parameters in response to the inputted docking parameters;
and generating an output file according to each molecular docking result, and outputting the output file so as to display the output file at the front end of the visual platform.
2. The molecular docking method of claim 1, wherein at least one molecular docking result is generated based on the ligand input information, the receptor input information, and the docking parameters in response to the input docking parameters, and thereafter further comprising:
judging the state of the molecular docking result based on a preset judgment rule;
processing the molecular docking result according to the state of the molecular docking result, and generating the output file based on the processed molecular docking result;
wherein the state of the molecular docking result comprises docking success or docking failure.
3. The molecular docking method according to claim 2, wherein the processing of the molecular docking result according to the state of the molecular docking result and the generation of the output file based on the processed molecular docking result specifically include:
if the molecular docking result is judged to be successfully docked, calculating the molecular parameters of the ligand molecules to obtain ligand parameter information, and reconstructing the chemical bonds of the ligand molecules;
and combining the ligand parameter information, the ligand molecules after chemical bond reconstruction and the receptor molecules to be used as the molecular docking result, and forming an output file.
4. The molecular docking method of claim 3, wherein the ligand parameter information comprises at least one of:
the ligand molecule has molecular weight, molecular formula, ring number, hydrogen bond donor number, hydrogen bond acceptor number, logP property, TPSA property and Lipinski property.
5. The molecular docking method according to claim 2, wherein if it is determined that the state of the molecular docking result is a docking failure, the ligand input information and the receptor input information are used as the molecular docking result, and an output file is formed.
6. A molecular docking method based on an AutoDock visual platform is applied to the front end of the visual platform, and is characterized by comprising the following steps:
acquiring an output file, and displaying the output file in an image form;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structural information of ligand molecules; the receptor input information is information in a preset format generated according to structural information of receptor molecules.
7. A molecular docking system based on an AutoDock visual platform is applied to the back end of the visual platform, and is characterized in that the system comprises:
an information acquisition unit for acquiring structural information of the ligand molecule and structural information of the receptor molecule;
the input file generating unit is used for generating ligand input information in a preset format according to the structural information of the ligand molecules and generating receptor input information in a preset format according to the structural information of the receptor molecules;
a docking result generation unit for generating at least one molecular docking result based on the ligand input information, the receptor input information and the docking parameters in response to the inputted docking parameters;
and the file output unit is used for generating an output file according to each molecular docking result and outputting the output file so as to display the output file at the front end of the visual platform.
8. A molecule docking system based on an AutoDock visual platform is applied to the front end of the visual platform, and is characterized in that the system comprises:
the output file display unit is used for acquiring an output file and displaying the output file in an image form;
wherein the output file is generated according to the molecular docking result; the molecular docking result is generated by the back end of the visualization platform in response to the inputted docking parameters based on the ligand input information, the receptor input information and the docking parameters; the ligand input information is information in a preset format generated according to the structure information of ligand molecules; the receptor input information is information in a preset format generated based on structural information of the receptor molecule.
9. An electronic device comprising a memory, a processor and a computer program stored on the memory and executable on the processor, characterized in that the processor implements the steps of the method according to any of claims 1 to 6 when executing the program.
10. A non-transitory computer-readable storage medium, on which a computer program is stored, which, when being executed by a processor, carries out the steps of the method according to any one of claims 1 to 6.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202210947895.4A CN115295091B (en) | 2022-08-08 | 2022-08-08 | Molecular docking method and system based on AutoDock visual platform |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202210947895.4A CN115295091B (en) | 2022-08-08 | 2022-08-08 | Molecular docking method and system based on AutoDock visual platform |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN115295091A true CN115295091A (en) | 2022-11-04 |
| CN115295091B CN115295091B (en) | 2023-09-01 |
Family
ID=83829076
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202210947895.4A Active CN115295091B (en) | 2022-08-08 | 2022-08-08 | Molecular docking method and system based on AutoDock visual platform |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN115295091B (en) |
Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20070020642A1 (en) * | 2003-07-03 | 2007-01-25 | Zhan Deng | Structural interaction fingerprint |
| CN114300039A (en) * | 2021-12-31 | 2022-04-08 | 中国医学科学院医学实验动物研究所 | Bioactive component screening system based on virus structural protein |
| US20220130487A1 (en) * | 2020-06-28 | 2022-04-28 | Shenzhen Jingtai Technology Co., Ltd. | Drug virtual screening system for crystal complexes, and method of using the same |
| CN114627960A (en) * | 2022-01-26 | 2022-06-14 | 深圳阿尔法分子科技有限责任公司 | Methods and systems for analyzing G-protein coupled receptor interactions with ligands |
-
2022
- 2022-08-08 CN CN202210947895.4A patent/CN115295091B/en active Active
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20070020642A1 (en) * | 2003-07-03 | 2007-01-25 | Zhan Deng | Structural interaction fingerprint |
| US20220130487A1 (en) * | 2020-06-28 | 2022-04-28 | Shenzhen Jingtai Technology Co., Ltd. | Drug virtual screening system for crystal complexes, and method of using the same |
| CN114300039A (en) * | 2021-12-31 | 2022-04-08 | 中国医学科学院医学实验动物研究所 | Bioactive component screening system based on virus structural protein |
| CN114627960A (en) * | 2022-01-26 | 2022-06-14 | 深圳阿尔法分子科技有限责任公司 | Methods and systems for analyzing G-protein coupled receptor interactions with ligands |
Non-Patent Citations (1)
| Title |
|---|
| 赵晨;夏春光;于敏;潘月;王辂;: "分子对接软件在药物设计中的应用", 中国抗生素杂志, no. 03 * |
Also Published As
| Publication number | Publication date |
|---|---|
| CN115295091B (en) | 2023-09-01 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| US20020046149A1 (en) | Apparatus, methods and articles of manufacture for constructing and executing computerized transaction processes and programs | |
| US10963888B2 (en) | Payment complaint method, device, server and readable storage medium | |
| CN111290951B (en) | Test method, terminal, server, system and storage medium | |
| CN109857404B (en) | SDK interface packaging method and device, storage medium and electronic equipment | |
| CN111190596A (en) | Joint debugging method and device, computer equipment and readable storage medium | |
| CN110289055B (en) | Method and device for predicting drug target, computer equipment and storage medium | |
| CN114092951A (en) | Financial bill processing method, device, system, equipment and medium combining RPA and AI | |
| CN111309991B (en) | Query statement generation method and device and data query method and system | |
| CN115295091B (en) | Molecular docking method and system based on AutoDock visual platform | |
| CN115061912A (en) | Test case generation and test method, system and medium | |
| TWI308700B (en) | ||
| Motta et al. | Actinide inverse trans influence versus cooperative pushing from below and multi-center bonding | |
| Maisonnave et al. | A better diagnostic of the load imbalance in OASIS based coupled systems | |
| CN109656817A (en) | A kind of automation interface test device and equipment | |
| WO2019076054A1 (en) | Time period selection method, apparatus, computer device, and storage medium | |
| KR20210155958A (en) | Method for providing dentistry image and dentistry image processing device therefor | |
| CN115629743A (en) | Service component arranging method, service scheduling method and device, electronic equipment and storage medium | |
| US11620322B1 (en) | System and method for managing regulatory information | |
| CN115629940A (en) | Micro-service full-link tracking method, device, system and medium | |
| CN108829028A (en) | Execute program creating method, processing method and device, medium, terminal | |
| CN112651620A (en) | System-level software demand processing method and device, terminal equipment and storage medium | |
| CN113674061A (en) | Bond inquiry transaction message docking method and device | |
| KR20160120366A (en) | The dimensional control system based on mobile | |
| Hu et al. | Windock: Structure‐based drug discovery on windows‐based PCs | |
| Bugnon et al. | SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant |