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Molecular docking method and device based on GPU acceleration

A molecular docking and molecular conformation technology, applied in molecular design, multi-programming device, resource allocation, etc., can solve problems such as slow docking speed and poor scoring ability, and achieve the effect of improving accuracy and reducing cost.

Pending Publication Date: 2022-07-22
NANJING UNIV OF POSTS & TELECOMM
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Problems solved by technology

[0008] The purpose of the present invention is to provide a molecular docking method and device based on GPU acceleration to solve the problems of poor scoring ability and slow docking speed of existing molecular docking methods and devices

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  • Molecular docking method and device based on GPU acceleration
  • Molecular docking method and device based on GPU acceleration
  • Molecular docking method and device based on GPU acceleration

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Embodiment Construction

[0085] In order to make the objectives, technical solutions and advantages of the present invention clearer, the present invention will be described in detail below with reference to the accompanying drawings and specific embodiments.

[0086] The invention provides a method and device for molecular docking based on GPU acceleration, and realizes the heterogeneous parallel structure of GPU and CPU of AutoDock Vina based on OpenCL, reduces the number of data transmissions between CPU and GPU, and reduces communication cost; Introduce Δ vina RF 20 Scoring and reordering the molecular conformation output by AutoDock Vina improves the accuracy of the output molecular conformation, making AutoDock Vina more suitable for virtual drug screening in real scenarios.

[0087] It should be noted that the GPU model used in the following embodiments is NVIDIA GeForce GTX 1060 6GB, and the CPU model is Intel(R) Core(TM) i7-8700 CPU@3.21GHz. Of course, in other embodiments, the GPU model An...

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Abstract

The invention discloses a molecular docking method and device based on GPU acceleration, and the method comprises the steps that a CPU end carries out data preparation and sets an OpenCL environment, the data preparation comprises docking box and parameter preparation of the docking box, and then data is transmitted to a GPU end; the GPU end calculates the interaction force between the atoms at the lattice points in the docking box and the atoms of the acceptor and generates a grid cache table; the CPU end generates a plurality of random molecular conformations of the ligand and transmits the random molecular conformations to the GPU end, and the GPU end optimizes the random molecular conformations by using a Monte Carlo iterative local search algorithm and scores the random molecular conformations to obtain conformations and transmits the conformations back to the CPU end; the CPU end optimizes and ranks the conformations; sequentially carrying out the optimization steps on all ligands in the ligand library; and the molecular conformations in the CPU end are scored and sorted by using a scoring function delta vinaRF20. According to the method, the conformations are re-scored and sorted through the delta vinaRF20, so that the accuracy of outputting the conformations is improved; according to the OpenCL-based AutoDock Vina heterogeneous parallel acceleration structure, the docking time is shortened, and the drug research and development cost is reduced.

Description

technical field [0001] The invention relates to a molecular docking method and device based on GPU acceleration, belonging to the field of hardware accelerated drug design. Background technique [0002] The development of new drugs usually requires testing a large-scale ligand library for a specific target. The binding mode and binding affinity between protein receptors and small molecule ligands can be predicted by molecular docking software, and the binding affinity of the bound compound. Sort to reduce the number of ligands for subsequent in vivo and in vitro testing. [0003] AutoDock Vina is the most commonly used open source docking software in the field of molecular docking. In the CASF-2016 scoring function comparison evaluation, AutoDock Vina is the software with the highest docking ability among all molecular docking tools. AutoDock Vina uses the gradient-based optimizer BFGS and the Monte Carlo-based iterative local search algorithm, which effectively improves th...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16C20/50G16C20/90G16C20/70G16C10/00G06F9/50
CPCG16C20/50G16C20/90G16C20/70G16C10/00G06F9/5027Y02D10/00
Inventor 吴建盛朱翔宇丁季唐诗迪胡海峰
Owner NANJING UNIV OF POSTS & TELECOMM