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公开(公告)号：US11609807B2
公开(公告)日：2023-03-21
申请号：US16630467
申请日：2018-12-21
发明人： Yongpan Chen , Yang Liu , Wanchao Zhang , Cuihua Song , Fei Han , Shuhao Wen , Jian Ma , Lipeng Lai
摘要： The invention belongs to the technical field of the molecular force field and particularly relates to a computing task management and analysis system for molecular force field parameter building and an operation method thereof. The system comprises a computing result analysis module and a computing task management module, the computing result analysis module is connected with the computing task management module, and the computing task management module is connected with a force field building computing server through a cloud computing interface. The operation method comprises: (1) selecting a molecular force field building computing templates; (2) selecting a computing task submitting platform and submitting computing tasks; (3) retrieving computing results; and (4) analyzing the computing results. According to the invention, since force field building system users mainly including researchers do not have powerful open interface development capacity commonly, a convenient cloud computing calling interface is provided, and the force field building speed is improved; the system provides full-view and visual effects; an interactive analysis mode is provided for the force field building computing results, which facilitates quick location of a computing exception; and automatic task processing and analysis are supported.
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公开(公告)号：US11562809B2
公开(公告)日：2023-01-24
申请号：US16629959
申请日：2018-12-25
发明人： Huanhuai Zhang , Guangxu Sun , Yang Liu , Shuhao Wen , Jian Ma , Lipeng Lai
摘要： A method for automatically generating a universal set of stereoisomers of an organic molecule. The method includes: (1) segmenting an input molecule into a group of fragments; (2) matching the obtained isomer fragments with fragment templates in a fragment template library; (3) generating all isomers of the corresponding fragments according to fragment template information; and (4) traversing all the isomer fragments and sites thereof, and assembling the fragments at the two ends of a broken bond in the step (1) according to all possible sites of a broken-bond atom to obtain all stereoisomers; and if filtering is needed, performing filtering according to a specified filtering rule.
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公开(公告)号：US11443834B2
公开(公告)日：2022-09-13
申请号：US16466645
申请日：2018-05-09
发明人： Yang Liu , Peiyu Zhang , Mingjun Yang , Guangxu Sun , Jian Ma , Lipeng Lai , Shuhao Wen
摘要： The invention relates to an automatic conformation analysis method for quasi-drug organic molecules. The method includes: extracting a group of fragments from an input molecule, wherein there are primarily three types of fragments: a flexible bond fragment, a ring isomerism fragment and a conformation isomerism fragment; carrying out knowledge-based conformation recommendation; carrying out conformation recommendation based on force field scanning; verifying, by QM, the generated conformations, wherein if the verification succeeds, it indicates that the recommended conformations are valid; or otherwise, the force field is corrected; collecting conformation lists of the fragments; and combining and optimizing conformation parameters of the fragments through a genetic algorithm, and finding out a set of optimal conformations. The invention integrates the advantages of a knowledge-based method and the advantages of a computation method, so that accurate conformation recommendations can be acquired.
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公开(公告)号：US20220246238A1
公开(公告)日：2022-08-04
申请号：US17617594
申请日：2020-05-29
发明人： Chao CHANG , Jian MA , Lipeng LAI , Shuhao WEN
摘要： A method of atomic sequence rearrangement, includes the following steps. Topological rearrangement: the atomic sequence of the target structure is rearranged referring to the reference structure using the two-dimensional topological rearrangement method. Judgment of equivalent atoms: judge the equivalent atoms in the topological structure. Measuring and marking: mark the atomic chiral information of the rearranged structure and the reference structure. Second rearrangement: refer to the reference structure for the second rearrangement of the atomic sequence for the rearranged structure.
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公开(公告)号：US20220189586A1
公开(公告)日：2022-06-16
申请号：US17432092
申请日：2020-07-08
发明人： Hongrui LIN , Mingjun YANG , Chunwang PENG , Chunan WU , Jian MA , Shuhao WEN , Lipeng LAI
摘要： The present invention provides a molecular force field multi-objective fitting algorithm library and the workflow, including: FFOptlterator as the main module for input and output and force field parameter training iteration; EnergyCalculator module used for MM energy and energy derivatives calculation for the required value of each iteration in the optimization algorithm; the PropertyEstimator module used for the thermodynamic property calculation based on the MD simulation. Wherein, when initializing the FFOptlterator and EnergyCalculator objects, the user specifies the training force field parameters, adjustable parameter ranges, system setting arguments, and MD simulation parameters. The invention is suitable for the related applications of molecular force field training and verification, and implement the framework for different training targets, the prediction of different molecular physical properties, the compatibility and conversion of force field parameters in different formats, integration of multi-objective optimization, result analysis and graphing, etc.
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6.发明申请公开(公告)号：US20220115094A1
公开(公告)日：2022-04-14
申请号：US17266115
申请日：2020-02-25
发明人： Zenghui LIU , Mi HE , Mingjun YANG , Lipeng LAI , Jian MA , Shuhao WEN
摘要： The invention provides a free energy perturbation computation scheduling method used in a heterogeneous cluster environment, including the following steps. Step A: performing npt ensemble dynamic simulations through pre-built molecular/protein structures and input files to obtain equilibrium structures; Step B: running replica exchange dynamic calculations based on Hamiltonian to obtain enough trajectory data; Step C: analyzing trajectory files, and combining the trajectory files with various prmtop to generate new amber calculation inputs, calculating a single point energy corresponding to each conformation after combination; Step D: using regular expressions to extract energy values from log files, and at the same time cleaning up intermediate temporary files to complete a calculation process of a single molecule.
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公开(公告)号：US20210365618A1
公开(公告)日：2021-11-25
申请号：US17055605
申请日：2019-10-17
发明人： Bai XUE , Jian MA , Lipeng LAI , Shuhao WEN , Peiyu ZHANG
摘要： The disclosure provides an efficient Monte Carlo molecular simulation method for calculating the liquid phase interfacial tension between benzene and water by improving Ewald sum, including the following steps: Step A: Initialize the simulation: two simulation boxes were prepared, both with the size (30×30×45 Å)-(35×35×55 Å), and 1200-2000 water molecules and 230-380 benzene molecules were respectively put on the grid point of the two boxes; Step B: Select the force field used for simulation; Step C: Perform Monte Carlo simulations on the two boxes separately under the canonical ensemble; Step D: Join the water box and the benzene box along the z direction to form a large box of (30×30×90 Å)-(35×35×110 Å), and run 50000-80000 Monte Carlo cycles to make the system reach equilibrium; Step E: After the system reaches equilibrium, the data was collected during the production period.
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公开(公告)号：US20210200536A1
公开(公告)日：2021-07-01
申请号：US17263157
申请日：2019-12-31
发明人： Bingkun LI , Liang TAN , Chunan WU , Jian MA , Lipeng LAI , Shuhao WEN
摘要： A drug research and development software repository and a software package management system. The drug research and development software repository includes a user authentication module, a software package upload and index creation module, a baseline release management module, an authorization management module, a software package retrieval and download module, an adapter plug-in, and a storage layer. The software package management system includes an authentication module, a package management service module, a web front-end module, and a command line tool module. Various object storage services can be connected to software repositories through a plug-in mode, thereby realizing cross-platform, and multi-development language software package management; authentication and authorization function are added in making the software distribution more concise; the baseline management function is added in to make the software release more concise, and improve the collaboration efficiency of internal developers in the development of different software packages of the same software system.
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公开(公告)号：US20200312427A1
公开(公告)日：2020-10-01
申请号：US16482704
申请日：2018-05-11
发明人： Qun ZENG , Peiyu ZHANG , Yingdi JIN , Jian MA , Lipeng LAI , Shuhao WEN
IPC分类号： G16C10/00
摘要： A method for automatically and efficiently fitting repulsive potentials through DFTB includes: optimizing a molecule containing an atomic pair, and performing spacing scan on the atomic pair according to an acting interval of repulsive potentials; performing high-accuracy energy calculation on a scanning result; performing difference calculation on obtained energy to obtain second-order derivatives of force and energy; saving a structure, the energy, the second-order derivatives of force and energy into a database; acquiring energy without a repulsive potential as well as the second-order derivatives of force and energy to obtain target values of the repulsive potentials; transforming the separated target values of the repulsive potentials into splines; splicing multiple splines on a mean position between equilibrium position points to obtain new train data; constructing a train set by means of necessary samples and choosable samples; and fitting the repulsive potentials through singular value decomposition.
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10.发明授权公开(公告)号：US11609758B2
公开(公告)日：2023-03-21
申请号：US17263157
申请日：2019-12-31
发明人： Bingkun Li , Liang Tan , Chunan Wu , Jian Ma , Lipeng Lai , Shuhao Wen
摘要： A drug research and development software repository and a software package management system. The drug research and development software repository includes a user authentication module, a software package upload and index creation module, a baseline release management module, an authorization management module, a software package retrieval and download module, an adapter plug-in, and a storage layer. The software package management system includes an authentication module, a package management service module, a web front-end module, and a command line tool module. Various object storage services can be connected to software repositories through a plug-in mode, thereby realizing cross-platform, and multi-development language software package management; authentication and authorization function are added in making the software distribution more concise; the baseline management function is added in to make the software release more concise, and improve the collaboration efficiency of internal developers in the development of different software packages of the same software system.
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