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© Research
Publication : Bioinformatics (Oxford, England)

Grid computing for improving conformational sampling in NMR structure calculation

Team: Functional dynamics
Team: Structural Bioinformatics
Member: Fabien Mareuil
Member: Thérèse Malliavin
Member: Michael Nilges
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics (Oxford, England) - 05 May 2011

Mareuil F, Blanchet C, Malliavin TE, Nilges M

Link to Pubmed [PMID] – 21546391

Bioinformatics 2011 Jun;27(12):1713-4

MOTIVATION: Methods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes.

RESULTS: Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power.

AVAILABILITY: The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.