High-Throughput parallel blind Virtual Screening using BINDSURF

BMC Bioinformatics

Research

Horacio Pérez-Sánchez¹  José M García¹  Irene Sánchez-Linares¹  José M Cecilia¹ 

[1] Computer Engineering Department, School of Computer Science, University of Murcia, Spain;

关键词: Shared Memory;    Virtual Screening;    Global Memory;    Docking Simulation;    Texture Memory;   

DOI  :  10.1186/1471-2105-13-S14-S13

来源: Springer

【 摘 要 】

BackgroundVirtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, usually derived from the interpretation of the protein crystal structure. However, it has been demonstrated that in many cases, diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact.ResultsWe present BINDSURF, a novel VS methodology that scans the whole protein surface in order to find new hotspots, where ligands might potentially interact with, and which is implemented in last generation massively parallel GPU hardware, allowing fast processing of large ligand databases.ConclusionsBINDSURF is an efficient and fast blind methodology for the determination of protein binding sites depending on the ligand, that uses the massively parallel architecture of GPUs for fast pre-screening of large ligand databases. Its results can also guide posterior application of more detailed VS methods in concrete binding sites of proteins, and its utilization can aid in drug discovery, design, repurposing and therefore help considerably in clinical research.

【 授权许可】

Unknown   
© Sánchez-Linares et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.