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GPU parallel computing molecular similarity method, device and system and medium

A parallel computing and similarity technology, used in computing, multi-programming devices, and analyzing two-dimensional or three-dimensional molecular structures, etc., can solve problems for a long time, and achieve the effect of improving computing speed.

Pending Publication Date: 2022-05-20
深圳北鲲云计算有限公司
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Problems solved by technology

But even with the Gaussian optimization technique, ROCS takes a long time to complete when scanning a large compound database

Method used

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  • GPU parallel computing molecular similarity method, device and system and medium
  • GPU parallel computing molecular similarity method, device and system and medium
  • GPU parallel computing molecular similarity method, device and system and medium

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Embodiment Construction

[0042] In order to make the object, technical solution and effect of the present invention more clear and definite, the present invention will be further described in detail below. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

[0043] Such as Figure 1-2 Shown, a kind of GPU parallel computing molecular similarity method comprises the following steps:

[0044] S100, input query compound;

[0045] Extract from the database or custom build, input the compound to be queried, extract feature points based on the queried compound, and generate a search formula.

[0046] S200. Calculate the centroid of the query compound;

[0047] When calculating the 3D Gaussian superposition between the query compound and the compounds in the library, in order to ensure the accuracy of the calculation and improve the calculation speed, the query compound will be adjusted. In order to facil...

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Abstract

The invention discloses a GPU (Graphics Processing Unit) parallel computing molecular similarity method, device and system and a medium. The method comprises the following steps of: inputting a query compound; calculating the center of mass of the query compound; translating and / or rotating the query compound based on the center of mass; parallel computing is carried out through a GPU, and query compounds before and after transformation serve as initial search points to be compared with molecular compounds in a molecular library; and filtering according to a comparison calculation result, and outputting a molecular compound similar to the query compound.

Description

technical field [0001] The invention relates to the technical field of computer-aided drug research and development, in particular to a GPU parallel computing method, device, system and medium for molecular similarity. Background technique [0002] Drug R&D has the characteristics of large investment, high risk, and long cycle. Usually, a drug R&D cycle is more than 10 years, and the R&D investment is hundreds of millions of dollars, and it shows an upward trend year by year. Drug screening is a key link in drug discovery, and high-throughput drug virtual screening can greatly reduce screening time and cost, which is of great significance for accelerating drug development. Matching and quantitative comparison of the three-dimensional shapes and pharmacophores (groups of atoms in a molecule with specific properties) of two molecules to each other is a major approach in drug design. The molecular volume is related to the shape, and the shape determines the physicochemical pro...

Claims

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Application Information

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IPC IPC(8): G16B15/00G16B50/00G06F9/50G06F16/903
CPCG16B15/00G16B50/00G06F9/5072G06F16/90335
Inventor 冯建新李青松
Owner 深圳北鲲云计算有限公司
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