Shenzhen Jingtai Technology Co., Ltd.

Shenzhen Rentai Pharmatech Ltd

Shuhao Wen

Jian Ma

Lipeng Lai

Yang Liu

Peiyu Zhang

Guangxu Sun

Mingjun Yang

Xuekun Shi

Yan Wang

Fei Han

Liang Tan

Yongpan Chen

Jiajun Huang

Dongxu Yi

Guobin Ren

Hui Xiao

Qun Zeng

Li Ouyang

Shanshan Fan

Fenglei Cao

Yanqi Zhang

Shigang Ruan

Yingdi Jin

Chunwang Peng

Huanhuai Zhang

Chunan Wu

Bingkun Li

Cuihua Song

Wanchao Zhang

Bai Xue

Ziqi Jiang

Xiao Wan

The present invention provides a general description language data system for directed acyclic graph automatic task flow, including: Step definition layer, Workflow definition layer and Template definition layer; The Step definition layer is the description of a single task, for the input and output declarations of each docker image or other executor, comprises name, type, file and parameters. The Workflow definition layer is a workflow composed of one or more Steps, the dependency topology of these Steps needs to be defined, and shared parameters can also be defined. The Template definition layer is based on a Workflow definition layer. The Template definition layer pre-sets the parameters, and supplies the descriptions, checkers or data source definitions of the parameters. The data center of the present invention is used with the task execution tool, and a programming language needs to be used to implement the corresponding tool.

General description language data system for directed acyclic graph automatic task flow

A potential energy surface scanning method and system for the analysis of molecular conformational space includes: judge whether the molecule has adjacent dihedral angles. If there are adjacent dihedral angles, judge whether the adjacent dihedral angles are coupled by QM calculations. If they are judged not to be coupled, then perform one-dimensional potential energy scanning. If judged to be coupled, then perform MM coupling judgment. If the MM calculations determine that the adjacent dihedral angles are not coupled, a one-dimensional potential energy surface scan is performed. If the MM calculation judges that the adjacent dihedral angles are coupled, calculate the coverage of the extreme points on the two-dimensional potential energy surface by the combination of extreme points obtained by scanning the individual one-dimensional potential energy surfaces of the two dihedral angles according to the MM scanning result. If the coverage is good, then perform one-dimensional potential energy surface scanning.

Potential energy surface scanning method and system for molecular conformation space analysis

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.

Monte Carlo molecular simulation method for efficient calculation of the interfacial tension of water/benzene liquid phase by improving Ewald sum

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.

Computing task management and analysis system for molecular force field parameter building and operation method thereof

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.

Drug research and development software repository and software package management system

The invention belongs to the technical field of drug crystal analysis, and particularly relates to a drug crystal structure landscape analysis system and a landscape analysis method thereof. The drug crystal structure landscape analysis system calls a cloud computing interface to calculate the energy of input crystals through an algorithm deployed in the cloud in advance, and an energy-density space group landscape array diagram of the crystals is generated according to the computation results returned; and analysis is selectively carried out as needed, result reports arc analyzed and summarized as a final report, and the final report is converted into a text document. The drug crystal structure landscape analysis system and the landscape analysis method thereof satisfy the drug crystal structure analysis requirements in the new technology background, and can analyze a large quantity of crystals which are formed by a certain drug molecule and have different structures.

Drug crystal structure landscape analysis system and landscape analysis method thereof

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.

Method for automatically generating universal set of stereoisomers of organic molecule

This disclosure provides a system and method for user interaction in complex web 3D scenes, including a receiving module, a transmission module and a 3D model module. The receiving module receives molecular data. The transmission module analyzes the received molecular data and then enters the two branch modules at the same time. The branch modules include: a view layer unit: processing browser rendering and 3D model construction, the data generated by the branch will finally be presented on the browser page; a data layer unit: processing 3D picking-related business logic, and establishing a list of related model index information for atoms and covalent bonds in molecular data. The 3D model module: establishes a one-to-one correspondence between color and 3D model. This invention simplifies the display model of the molecule for the picking of web 3D molecular visualization and reduces the computational cost of the model data on the rendering.

System and method for user interaction in complex web 3D scenes

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.

Automatic conformation analysis method for quasi-drug organic molecules

The invention belongs to the technical field force fields and particularly provides an atom type definition system and an atom type matching method. The atom type definition system includes an atom type visual UI interface, an atom type matching module, an atom type data management module and an atom type format transformation module. The atom type data management module includes an atom type definition data package. The system and method can describe various complicated atomic chemical environments, the description capability is improved, and the computation of a force field can be more accurate. According to the invention, convenient operation on an atom type can be realized, and addition, deletion, modification, inquiry as well as statistics of multiple dimensions are very visual and convenient.

Atom type definition system and atom type matching method thereof

Forms B and C of (R)&#x2014;N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinolin-4-yl)cyclohexyl)propanamide are stable under the conditions of light, high temperature and high humidity.

Forms of (R)-N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinolin-4- yl)cyclohexyl)propanamide

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.

Method for automatically and efficiently fitting repulsive potentials through DFTB

A GROMACS cloud computing process control method includes the following steps. Step (1): acquire crystal structures having energy ranked at the top by cluster ranking, and then obtain a GROMACS structural file. Step (2): acquire optimal force field parameters, and then automatically convert the optical force field parameters into a GROMACS force field parameter file. Step (3): import the yoda library function to automatically generate a corresponding GROMACS simulation parameter file according to simulation types in different stages. Step (4): import a mixc library function to submit GROMACS computation and analysis tasks to a task scheduling platform called Majorana. Step (5): add a corresponding monitor task for the same batch of tasks for each structure, and acquire the execution status of the tasks in real time. Step (6): acquire corresponding analysis results from ArangoDB after all the tasks are executed, and directly plot corresponding curves in Jupyter.

GROMACS cloud computing process control method

The invention provides a scientific computing process management system. The system includes a basic data presentation layer for storing and presenting business models, a case service module for providing addition, deletion, checking, and changing as well as task submission and data analysis triggering of a case contained in an interface, computing service modules released as a packaged based image and called through a task scheduling system, a resource statistic service module for providing computing resource consumptions statistics accurate to a task level, a persistent layer for persisting data, an audit module for performing audit work on universal data changes and performing backtracking when data is in an unexpected state, a real-time sync module for performing data synchronization in real time together with the task scheduling system, an async communication module for processing computing service communication and an async analysis module for performing analysis in a pushing process of a case.

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Guangdong, China

Shuhao Wen