High-throughput virtual drug screening method based on dynamic data partitioning and conflict resolution

A conflict resolution, dynamic data technology, applied in electrical digital data processing, special data processing applications, for analyzing two-dimensional or three-dimensional molecular structures, etc., to achieve the effect of alleviating the pressure of instantaneous communication

Active Publication Date: 2018-01-19
NAT UNIV OF DEFENSE TECH
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Problems solved by technology

[0017] Aiming at the problem that the current mainstream high-throughput virtual screening method has unbalanced load, instantaneous IO, and communication bottlenecks caused by communication operations, which lead to the slow speed of the current mainstream high-throughput virtual screening method when performing virtual drug screening, the present invention provides a method based on The high-throughput drug virtual screening method of dynamic data division and conflict resolution aims to achieve load balancing of high-throughput virtual drug screening, solve massive concurrent IO and communication problems, improve the speed and efficiency of drug virtual screening, and shorten the research cycle of new drugs

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  • High-throughput virtual drug screening method based on dynamic data partitioning and conflict resolution
  • High-throughput virtual drug screening method based on dynamic data partitioning and conflict resolution

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Embodiment Construction

[0058] We chose the drug virtual screening software D 3 DOCKxb, for details, please refer to http: / / med.wanfangdata.com.cn / Paper / Detail? id=DegreePaper_Y2675158. D. 3 DOCKxb is a software for virtual screening of drugs. The software is jointly developed by Shanghai Institute of Materia Medica, Chinese Academy of Sciences and National University of Defense Technology. It supports CPU and MIC multi-thread parallelism. By using MPI technology combined with D 3 DOCKxb realizes the high-throughput drug virtual screening method of the present invention.

[0059] The Tianhe-2 supercomputer is our test platform and contains 16,000 computing nodes. Each computing node contains 2 Xeon E5 12-core multi-core CPUs and 3 Xeon Phi 57-core many-core accelerators, with a total of 3.12 million computing cores. Each node has 64GB of main memory, and each Xeon Phi coprocessor has 8GB of memory on board, so each node has a total of 88GB of memory, and the total memory is 1.408PB.

[0060] We...

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Abstract

The invention discloses a high-throughput medicine virtual screening method based on dynamic data partitioning and conflict resolution, and aims to improve medicine virtual screening speed and efficiency and shorten a new medicine research period. The technical scheme is that processes are grouped, tasks are divided into two parts, wherein the first part adopts static tasks to carry out division,each group leader process obtains screening operations in a rotation way, and the operations are distributed to group members; the second part adopts dynamic tasks to carry out division, a process grouping way is adopted, and the screening operations are dynamically obtained by the group leader of each group and are distributed to the group members through a principle of "able person should do more work"; and when the group member process processes the screening operation for the first time, sleeping is carried out for a certain time according to process numbers, and ''assembly line type'' IO(Input / Output) and communication hiding are realized. Compared with the traditional mainstream high-throughput medicine virtual screening method, the high-throughput medicine virtual screening methoddisclosed by the invention can effectively realize the load balance of high-throughput medicine virtual screening, solves the problems of mass concurrence IO and communication, improves medicine virtual screening speed and efficiency and shortens a new medicine research period.

Description

technical field [0001] The invention relates to a drug virtual screening method in the field of computer-aided drug design, in particular to a high-throughput drug virtual screening method based on dynamic data division and conflict resolution. Background technique [0002] Drug virtual screening is to use the molecular docking method with the help of computers to judge the activity of small molecules according to their ability to bind to proteins. High Throughput Virtual Screening is to use molecular docking technology in a short period of time, according to the molecular structure of the drug target, calculate the ability of small molecules in the compound library to bind to the target by means of molecular simulation, and predict candidate compounds physiological activity. High-throughput drug virtual screening has certain characteristics, mainly including: [0003] 1. There is a total job pool, or a job list, and each team member process obtains jobs from the job pool ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 彭绍亮程乾杨灿群卢宇彤刘杰吴诚堃顾祥高明刘欣王海强杨顺云
Owner NAT UNIV OF DEFENSE TECH
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