Developing a move-set for protein model refinement.
Identifieur interne : 003E38 ( Main/Exploration ); précédent : 003E37; suivant : 003E39Developing a move-set for protein model refinement.
Auteurs : Marc N. Offman [Royaume-Uni] ; Paul W. Fitzjohn ; Paul A. BatesSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2006.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Alignement de séquences (méthodes), Analyse de séquence de protéine (méthodes), Conception de logiciel (MeSH), Conformation des protéines (MeSH), Données de séquences moléculaires (MeSH), Déplacement (MeSH), Logiciel (MeSH), Modèles chimiques (MeSH), Modèles moléculaires (MeSH), Protéines (composition chimique), Simulation numérique (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Protéines.
- méthodes : Alignement de séquences, Analyse de séquence de protéine.
- Algorithmes, Conception de logiciel, Conformation des protéines, Données de séquences moléculaires, Déplacement, Logiciel, Modèles chimiques, Modèles moléculaires, Simulation numérique, Séquence d'acides aminés.
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
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Bates</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16705011</idno><idno type="pmid">16705011</idno><idno type="doi">10.1093/bioinformatics/btl192</idno><idno type="wicri:Area/Main/Corpus">003E03</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003E03</idno><idno type="wicri:Area/Main/Curation">003E03</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003E03</idno><idno type="wicri:Area/Main/Exploration">003E03</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Developing a move-set for protein model refinement.</title><author><name sortKey="Offman, Marc N" sort="Offman, Marc N" uniqKey="Offman M" first="Marc N" last="Offman">Marc N. Offman</name><affiliation wicri:level="1"><nlm:affiliation>Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories London, WC2A 3PX, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories London, WC2A 3PX</wicri:regionArea><wicri:noRegion>WC2A 3PX</wicri:noRegion></affiliation></author><author><name sortKey="Fitzjohn, Paul W" sort="Fitzjohn, Paul W" uniqKey="Fitzjohn P" first="Paul W" last="Fitzjohn">Paul W. Fitzjohn</name></author><author><name sortKey="Bates, Paul A" sort="Bates, Paul A" uniqKey="Bates P" first="Paul A" last="Bates">Paul A. Bates</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><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></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Alignement de séquences (méthodes)</term><term>Analyse de séquence de protéine (méthodes)</term><term>Conception de logiciel (MeSH)</term><term>Conformation des protéines (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Déplacement (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles chimiques (MeSH)</term><term>Modèles moléculaires (MeSH)</term><term>Protéines (composition chimique)</term><term>Simulation numérique (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Protéines</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence de protéine</term></keywords><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><term>Motion</term><term>Protein Conformation</term><term>Software</term><term>Software Design</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Conception de logiciel</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Déplacement</term><term>Logiciel</term><term>Modèles chimiques</term><term>Modèles moléculaires</term><term>Simulation numérique</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><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></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16705011</PMID><DateCompleted><Year>2006</Year><Month>09</Month><Day>05</Day></DateCompleted><DateRevised><Year>2009</Year><Month>11</Month><Day>04</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>15</Issue><PubDate><Year>2006</Year><Month>Aug</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Developing a move-set for protein model refinement.</ArticleTitle><Pagination><MedlinePgn>1838-45</MedlinePgn></Pagination><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="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.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The populus software package and the source code are available at http://bmm.cancerresearchuk.org/~offman01/populus.html.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Offman</LastName><ForeName>Marc N</ForeName><Initials>MN</Initials><AffiliationInfo><Affiliation>Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories London, WC2A 3PX, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fitzjohn</LastName><ForeName>Paul W</ForeName><Initials>PW</Initials></Author><Author ValidYN="Y"><LastName>Bates</LastName><ForeName>Paul A</ForeName><Initials>PA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>05</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="Y">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="Y">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009038" MajorTopicYN="N">Motion</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011506" MajorTopicYN="N">Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020539" MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012985" MajorTopicYN="N">Software Design</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>5</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>9</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>5</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16705011</ArticleId><ArticleId IdType="pii">btl192</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btl192</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><noCountry><name sortKey="Bates, Paul A" sort="Bates, Paul A" uniqKey="Bates P" first="Paul A" last="Bates">Paul A. Bates</name><name sortKey="Fitzjohn, Paul W" sort="Fitzjohn, Paul W" uniqKey="Fitzjohn P" first="Paul W" last="Fitzjohn">Paul W. Fitzjohn</name></noCountry><country name="Royaume-Uni"><noRegion><name sortKey="Offman, Marc N" sort="Offman, Marc N" uniqKey="Offman M" first="Marc N" last="Offman">Marc N. Offman</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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