Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
We describe predictions made using the Rosetta structure prediction methodology for both template‐based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all‐atom refinement could be ca...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2007, Vol.69 (S8), p.118-128 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Das, Rhiju Qian, Bin Raman, Srivatsan Vernon, Robert Thompson, James Bradley, Philip Khare, Sagar Tyka, Michael D. Bhat, Divya Chivian, Dylan Kim, David E. Sheffler, William H. Malmström, Lars Wollacott, Andrew M. Wang, Chu Andre, Ingemar Baker, David |
| description | We describe predictions made using the Rosetta structure prediction methodology for both template‐based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all‐atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template‐based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near‐atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all‐atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions. Proteins 2007. © 2007 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/prot.21636 |
| format | Article |
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For the first time, aggressive sampling and all‐atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template‐based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near‐atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all‐atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions. Proteins 2007. © 2007 Wiley‐Liss, Inc.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.21636</identifier><identifier>PMID: 17894356</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Algorithms ; all-atom refinement ; CASP ; Computational Biology - methods ; fragment insertion ; free modeling ; Models, Molecular ; Protein Conformation ; protein structure prediction ; Proteins - chemistry ; Rosetta ; Software ; template-based modeling ; Thermodynamics</subject><ispartof>Proteins, structure, function, and bioinformatics, 2007, Vol.69 (S8), p.118-128</ispartof><rights>Copyright © 2007 Wiley‐Liss, Inc.</rights><rights>(c) 2007 Wiley-Liss, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c2806-2d2d00b4fccbee25d00a168974d89e105b684a68aecd835c74651a107dcf52b93</citedby><cites>FETCH-LOGICAL-c2806-2d2d00b4fccbee25d00a168974d89e105b684a68aecd835c74651a107dcf52b93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprot.21636$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.21636$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,4024,27923,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17894356$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Das, Rhiju</creatorcontrib><creatorcontrib>Qian, Bin</creatorcontrib><creatorcontrib>Raman, Srivatsan</creatorcontrib><creatorcontrib>Vernon, Robert</creatorcontrib><creatorcontrib>Thompson, James</creatorcontrib><creatorcontrib>Bradley, Philip</creatorcontrib><creatorcontrib>Khare, Sagar</creatorcontrib><creatorcontrib>Tyka, Michael D.</creatorcontrib><creatorcontrib>Bhat, Divya</creatorcontrib><creatorcontrib>Chivian, Dylan</creatorcontrib><creatorcontrib>Kim, David E.</creatorcontrib><creatorcontrib>Sheffler, William H.</creatorcontrib><creatorcontrib>Malmström, Lars</creatorcontrib><creatorcontrib>Wollacott, Andrew M.</creatorcontrib><creatorcontrib>Wang, Chu</creatorcontrib><creatorcontrib>Andre, Ingemar</creatorcontrib><creatorcontrib>Baker, David</creatorcontrib><title>Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>We describe predictions made using the Rosetta structure prediction methodology for both template‐based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all‐atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template‐based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near‐atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all‐atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions. Proteins 2007. © 2007 Wiley‐Liss, Inc.</description><subject>Algorithms</subject><subject>all-atom refinement</subject><subject>CASP</subject><subject>Computational Biology - methods</subject><subject>fragment insertion</subject><subject>free modeling</subject><subject>Models, Molecular</subject><subject>Protein Conformation</subject><subject>protein structure prediction</subject><subject>Proteins - chemistry</subject><subject>Rosetta</subject><subject>Software</subject><subject>template-based modeling</subject><subject>Thermodynamics</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kMtOGzEUQC1UVAJ00w-ovOoCacAejx-zK0QQkBCkSVA2SJbHcwfcziPYHh5_z0AC3XV1daVzj64OQt8pOaSEpEcr38XDlAomttCIklwmhLLsCxoRpWTCuOI7aDeEP4QQkTPxFe1QqfKMcTFCt_Poext7D3jloXQ2uq7FVefx-Hg-lTgafwcx4D649g7Dc4Q2uEfApq4TE7sGe6hcCw20ET-5eI9nXYAYza_7roF9tF2ZOsC3zdxDN2eni_F5cnk9uRgfXyY2VUQkaZmWhBRZZW0BkPJhMVSoXGalyoESXgiVGaEM2FIxbmUmODWUyNJWPC1ytod-rr1DiYceQtSNCxbq2rTQ9UELxZmgWTqAB2vQ-i6E4XW98q4x_kVTot9a6reW-r3lAP_YWPuigfIfuok3AHQNPLkaXv6j0tPZ9eJDmqxvXIjw_Hlj_F8tJJNcL68mOjvjy-nJb6In7BX3lY9v</recordid><startdate>2007</startdate><enddate>2007</enddate><creator>Das, Rhiju</creator><creator>Qian, Bin</creator><creator>Raman, Srivatsan</creator><creator>Vernon, Robert</creator><creator>Thompson, James</creator><creator>Bradley, Philip</creator><creator>Khare, Sagar</creator><creator>Tyka, Michael D.</creator><creator>Bhat, Divya</creator><creator>Chivian, Dylan</creator><creator>Kim, David E.</creator><creator>Sheffler, William H.</creator><creator>Malmström, Lars</creator><creator>Wollacott, Andrew M.</creator><creator>Wang, Chu</creator><creator>Andre, Ingemar</creator><creator>Baker, David</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></search><sort><creationdate>2007</creationdate><title>Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home</title><author>Das, Rhiju ; 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| subjects | Algorithms all-atom refinement CASP Computational Biology - methods fragment insertion free modeling Models, Molecular Protein Conformation protein structure prediction Proteins - chemistry Rosetta Software template-based modeling Thermodynamics |
| title | Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home |
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