Grid computing for improving conformational sampling in NMR structure calculation.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 21546391.
- Also identified by DOI 10.1093/bioinformatics/btr255.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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. 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. The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.
Medical subject headings
- Nuclear Magnetic Resonance, Biomolecular
- Protein Conformation
- Software