PoplarV1, Main, Corpus, bibRecord, 003E03

Developing a move-set for protein model refinement.

Identifieur interne : 003E03 ( Main/Corpus ); précédent : 003E02; suivant : 003E04

Developing a move-set for protein model refinement.

Auteurs : Marc N. Offman ; Paul W. Fitzjohn ; Paul A. Bates

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2006.

RBID : pubmed:16705011

English descriptors

KwdEn :
- Algorithms (MeSH), Amino Acid Sequence (MeSH), Computer Simulation (MeSH), Models, Chemical (MeSH), Models, Molecular (MeSH), Molecular Sequence Data (MeSH), Motion (MeSH), Protein Conformation (MeSH), Proteins (chemistry), Sequence Alignment (methods), Sequence Analysis, Protein (methods), Software (MeSH), Software Design (MeSH).
MESH :
- chemical , chemistry : Proteins.
- methods : Sequence Alignment, Sequence Analysis, Protein.
- Algorithms, Amino Acid Sequence, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Motion, Protein Conformation, Software, Software Design.

Abstract

MOTIVATION

A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model.

RESULTS

We describe here a number of refinement operators (collectively, 'move-set') that enable a relatively large region of conformational space to be searched. This is used within a genetic algorithm that reshuffles and repacks structural components. The utility of the move-set is demonstrated by introducing a cost function, containing both physical and other components guiding the input structures towards the target structure. We show that our move-set has the potential to improve the conformation of models and that this improvement can be beyond even the best template for some comparative modelling targets.

AVAILABILITY

The populus software package and the source code are available at http://bmm.cancerresearchuk.org/~offman01/populus.html.

DOI: 10.1093/bioinformatics/btl192
PubMed: 16705011

Links to Exploration step

pubmed:16705011

Le document en format XML

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<author><name sortKey="Offman, Marc N" sort="Offman, Marc N" uniqKey="Offman M" first="Marc N" last="Offman">Marc N. Offman</name>
<affiliation><nlm:affiliation>Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories London, WC2A 3PX, UK.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Fitzjohn, Paul W" sort="Fitzjohn, Paul W" uniqKey="Fitzjohn P" first="Paul W" last="Fitzjohn">Paul W. Fitzjohn</name>
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<author><name sortKey="Bates, Paul A" sort="Bates, Paul A" uniqKey="Bates P" first="Paul A" last="Bates">Paul A. Bates</name>
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<term>Amino Acid Sequence (MeSH)</term>
<term>Computer Simulation (MeSH)</term>
<term>Models, Chemical (MeSH)</term>
<term>Models, Molecular (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Motion (MeSH)</term>
<term>Protein Conformation (MeSH)</term>
<term>Proteins (chemistry)</term>
<term>Sequence Alignment (methods)</term>
<term>Sequence Analysis, Protein (methods)</term>
<term>Software (MeSH)</term>
<term>Software Design (MeSH)</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Alignment</term>
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<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Amino Acid Sequence</term>
<term>Computer Simulation</term>
<term>Models, Chemical</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
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<front><div type="abstract" xml:lang="en"><p><b>MOTIVATION</b>
</p>
<p>A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>We describe here a number of refinement operators (collectively, 'move-set') that enable a relatively large region of conformational space to be searched. This is used within a genetic algorithm that reshuffles and repacks structural components. The utility of the move-set is demonstrated by introducing a cost function, containing both physical and other components guiding the input structures towards the target structure. We show that our move-set has the potential to improve the conformation of models and that this improvement can be beyond even the best template for some comparative modelling targets.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>AVAILABILITY</b>
</p>
<p>The populus software package and the source code are available at http://bmm.cancerresearchuk.org/~offman01/populus.html.</p>
</div>
</front>
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<DateRevised><Year>2009</Year>
<Month>11</Month>
<Day>04</Day>
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<Title>Bioinformatics (Oxford, England)</Title>
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Developing a move-set for protein model refinement.

Developing a move-set for protein model refinement.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki