Abstract: 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.

Abstract: 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 ?)-(35×35×55 ?), 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 ?)-(35×35×110 ?), 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.

Abstract: The present disclosure relates to a heterocyclic amide derivative, a preparation method therefor and an application thereof. Specifically, the present disclosure relates to a compound of formula I, a preparation method therefor and an application thereof, a pharmaceutical composition containing the compound as an active ingredient, or a pharmaceutically acceptable salt thereof. The present disclosure further relates to a use of the compound of formula (I) in the treatment and prevention of EP4-mediated diseases.

Abstract: Disclosed are a pyrazolo[1,5-a]pyridine compound, a preparation method therefor and a use thereof. Also disclosed is a pharmaceutical composition containing the compound as an active ingredient or a pharmaceutically acceptable salt thereof. The present invention further relates to the use of a compound of formula (I) for treating and preventing diseases that can be treated with wild-type, gene fusion-type and mutant (including but not limited to G804 and G810) RET kinase inhibitors, including diseases or conditions mediated by an RET kinase.

Abstract: The present invention relates to a pyrazolo[1,5-a]pyridine derivative, a preparation method therefor, and a composition and a use thereof. Specifically, the present invention relates to the compound of formula (I) and the use thereof for the treatment and/or prevention of wild type, gene-fusion type (including but not limited to KIF5B, CCDC6 and NCOA4) and mutant type (including but not limited to V804, G810 and M918) RET kinases-related diseases, including diseases or conditions mediated by RET kinase.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: The present invention provides a method for testing and fitting the dihedral angle parameters in force field. The method first generates some representative conformations, and then compares the results of force field and quantum mechanics methods using these structures. If the results meet the predefined standards, the process ends; otherwise the molecule will be cut into small-size molecular fragments with only one flexible dihedral angle in each fragment. The dihedral angles will be scanned. And results of force field and quantum mechanics will be compared for each scanned flexible dihedral angle to find out those that do not meet the standards, and their parameters will be selected for further fitting. After new dihedral angle parameters are obtained, apply them to the original series of conformers of the whole molecule for validation. If results meet the standards, complete the whole process of testing and fitting poorly performing dihedral angle parameters.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: The present invention provides a drug virtual screening system for crystal complexes, and method of using the same, comprising a visualization subsystem, an evaluation tool box subsystem, an AI model management subsystem, a large-scale sampling subsystem, a virtual screening subsystem, and a data log storage subsystem. Starting with the known crystal complexes, a batch of candidate compounds that meet the requirements are recommended after going through the visualization subsystem, evaluation tool box subsystem, AI model management subsystem, large-scale sampling subsystem, and virtual screening system in turn. Based on this system, the generation of the compound library is organically combined with the subsequent virtual screening. Users only need to describe the action mode of the drug on the protein and the requirements for the drug to generate a batch of compounds that meet the expectations. The automated system reduces user intervention and improves the efficiency of research and development.

Abstract: 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.

Abstract: 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.

Abstract: The invention provides a reconciliation system and method based on a hybrid cloud computing platform. The reconciliation system includes: a bill data processing module, processing data from a public cloud billing API or downloaded bill detailed files; a data monitoring processing module, processing the data collected from the resource pool of the computing management system resource pool and task resource requested; a task data processing module obtaining and processing task data from the task database of the computing scheduling system, and calculating the core hours that the tasks consumed; a statistical alarm module combining the resource data table obtained by the above three modules to obtain the utilization ratio and difference range of the computing task packing can realize the reconciliation alarm and prediction for task core hours. The computing power demand for a large number of existing tasks can be used to guide the purchase of computing power in the future.

Abstract: 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.