Docking and Biomolecular Simulations on Computer Grids: Status and Trends

Title: Docking and Biomolecular Simulations on Computer Grids: Status and Trends

Volume: 4 Issue: 3

Author(s): Alexandru-Adrian Tantar, Sebastien Conilleau, Benjamin Parent, Nouredine Melab, Lorraine Brillet, Sylvaine Roy, El-Ghazali Talbi and Dragos Horvath

Affiliation:

Keywords: Large-scale parallel computing, molecular simulations, protein folding, conformational sampling, docking, computer- aided drug design

Abstract: This article outlines the recent developments in the field of large-scale parallel computing applied to molecular simulations, also including some original, preliminary contributions of the authors. It is not meant to be an exhaustive review paper, but rather an introductive material aimed at narrowing the “cultural gap” between the developers and users of molecular simulations (chemists, medicinal chemists and biologists – typical workstation users) and the informatics experts in massively parallel computing. The article starts with a brief overview of the existing molecular simulation techniques, in emphasizing the weaknesses of present approaches and the need for more computer-intensive methods. Docking procedures are the most discussed, given the high importance of this application in computer-aided drug design. An introduction to computer grids is logically pursued with the presentation of some of the most promising large-scale parallel molecular simulations already performed. Eventually, the authors own research program, Docking@Grid, is briefly discussed.

Cite this article as:

Tantar Alexandru-Adrian, Conilleau Sebastien, Parent Benjamin, Melab Nouredine, Brillet Lorraine, Roy Sylvaine, Talbi El-Ghazali and Horvath Dragos, Docking and Biomolecular Simulations on Computer Grids: Status and Trends, Current Computer-Aided Drug Design 2008; 4 (3) . https://dx.doi.org/10.2174/157340908785747438