Shenzhen Jingtai Technology Co., Ltd.

Shenzhen Rentai Pharmatech Ltd

Guangxu Sun

Jian Ma

Shuhao Wen

Lipeng Lai

Mingjun Yang

Yang Liu

Peiyu Zhang

Xuekun Shi

Jiajun Huang

Dongxu Yi

Guobin Ren

Hui Xiao

Li Ouyang

Huanhuai Zhang

Xiao Wan

Fenglei Cao

Yanqi Zhang

Shigang Ruan

Chunwang Peng

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

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

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 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

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Guangdong, China

Guangxu Sun