Building and assessing atomic models of proteins from structural templates: Learning and benchmarks
One approach to predict a protein fold from a sequence (a target) is based on structures of related proteins that are used as templates. We present an algorithm that examines a set of candidates for templates, builds from each of the templates an atomically detailed model, and ranks the models. The...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2009-09, Vol.76 (4), p.930-945 |
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| container_end_page | 945 |
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| container_issue | 4 |
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| container_title | Proteins, structure, function, and bioinformatics |
| container_volume | 76 |
| creator | Vallat, Brinda Kizhakke Pillardy, Jaroslaw Májek, Peter Meller, Jaroslaw Blom, Thomas Cao, BaoQiang Elber, Ron |
| description | One approach to predict a protein fold from a sequence (a target) is based on structures of related proteins that are used as templates. We present an algorithm that examines a set of candidates for templates, builds from each of the templates an atomically detailed model, and ranks the models. The algorithm performs a hierarchical selection of the best model using a diverse set of signals. After a quick and suboptimal screening of template candidates from the protein data bank, the current method fine‐tunes the selection to a few models. More detailed signals test the compatibility of the sequence and the proposed structures, and are merged to give a global fitness measure using linear programming. This algorithm is a component of the prediction server LOOPP (http://www.loopp.org). Large‐scale training and tests sets were designed and are presented. Recent results of the LOOPP server in CASP8 are discussed. Proteins 2009. © 2009 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/prot.22401 |
| format | Article |
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Proteins 2009. © 2009 Wiley‐Liss, Inc.</description><subject>Algorithms</subject><subject>Computer Simulation</subject><subject>feature selection</subject><subject>homology modeling</subject><subject>mathematical programming</subject><subject>Models, Molecular</subject><subject>Protein Folding</subject><subject>Proteins - chemistry</subject><subject>Structural Homology, Protein</subject><subject>structure determination</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU1v1DAQhi0Eokvhwg9AOXFASvFn7HBAaitYkFYtgiIkLpZjT1pDEm9tB9p_X293W-DCybL8zDOvZxB6TvABwZi-XseQDyjlmDxAC4JbWWPC-EO0wErJmgkl9tCTlH5gjJuWNY_RHmkZbbiQC2SPZj84P51XZnKVSQlSur3lMHpbjcHBkKrQV5sm4KdU9TGMVcpxtnmOZqgyjOvBZEhvqhWYON25OpjsxWjiz_QUPerNkODZ7txHX9-_Ozv-UK9Olx-PD1e1FZSSumugFVJwLhqLHXFC9Io74TAFoUCYrlWCN9ZKZaRS5QPOCdY3gInlnWop20dvt9713I3gLEy5BNTr6EuMax2M1_--TP5Cn4dfmkrSYoqL4OVOEMPlDCnr0ScLw2AmCHPSjRSspGMFfLUFbQwpRejvmxCsNzvRm3Hp250U-MXfsf6guyUUgGyB336A6_-o9KfPp2d30npb41OGq_uaMu6Skkmhv50sNV8uv7TNCdff2Q3tZqja</recordid><startdate>200909</startdate><enddate>200909</enddate><creator>Vallat, Brinda Kizhakke</creator><creator>Pillardy, Jaroslaw</creator><creator>Májek, Peter</creator><creator>Meller, Jaroslaw</creator><creator>Blom, Thomas</creator><creator>Cao, BaoQiang</creator><creator>Elber, Ron</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>200909</creationdate><title>Building and assessing atomic models of proteins from structural templates: Learning and benchmarks</title><author>Vallat, Brinda Kizhakke ; Pillardy, Jaroslaw ; Májek, Peter ; Meller, Jaroslaw ; Blom, Thomas ; Cao, BaoQiang ; Elber, Ron</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5221-b6e95754456c0d1d55f84d5d02e58e5ab98546cc78a788326dd53f6e01c4b8923</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Algorithms</topic><topic>Computer Simulation</topic><topic>feature selection</topic><topic>homology modeling</topic><topic>mathematical programming</topic><topic>Models, Molecular</topic><topic>Protein Folding</topic><topic>Proteins - chemistry</topic><topic>Structural Homology, Protein</topic><topic>structure determination</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vallat, Brinda Kizhakke</creatorcontrib><creatorcontrib>Pillardy, Jaroslaw</creatorcontrib><creatorcontrib>Májek, Peter</creatorcontrib><creatorcontrib>Meller, Jaroslaw</creatorcontrib><creatorcontrib>Blom, Thomas</creatorcontrib><creatorcontrib>Cao, BaoQiang</creatorcontrib><creatorcontrib>Elber, Ron</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vallat, Brinda Kizhakke</au><au>Pillardy, Jaroslaw</au><au>Májek, Peter</au><au>Meller, Jaroslaw</au><au>Blom, Thomas</au><au>Cao, BaoQiang</au><au>Elber, Ron</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Building and assessing atomic models of proteins from structural templates: Learning and benchmarks</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2009-09</date><risdate>2009</risdate><volume>76</volume><issue>4</issue><spage>930</spage><epage>945</epage><pages>930-945</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>One approach to predict a protein fold from a sequence (a target) is based on structures of related proteins that are used as templates. 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| identifier | ISSN: 0887-3585 |
| ispartof | Proteins, structure, function, and bioinformatics, 2009-09, Vol.76 (4), p.930-945 |
| issn | 0887-3585 1097-0134 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2719020 |
| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Algorithms Computer Simulation feature selection homology modeling mathematical programming Models, Molecular Protein Folding Proteins - chemistry Structural Homology, Protein structure determination |
| title | Building and assessing atomic models of proteins from structural templates: Learning and benchmarks |
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