Geometry-based flexible and symmetric protein docking
We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in...
Gespeichert in:
| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2005-08, Vol.60 (2), p.224-231 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 231 |
|---|---|
| container_issue | 2 |
| container_start_page | 224 |
| container_title | Proteins, structure, function, and bioinformatics |
| container_volume | 60 |
| creator | Schneidman-Duhovny, Dina Inbar, Yuval Nussinov, Ruth Wolfson, Haim J. |
| description | We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/prot.20562 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_67987748</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>17339762</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3962-f77e398ab9832a8b36f95d98abd611e3af48d2a1098a90e9f49861eb7929efdd3</originalsourceid><addsrcrecordid>eNqFkE1Pg0AQhjdGY2v14g8wnDyYUPcD9uNoqq0m1Rqtetws7GCwUCpLY_n3glS96WmSmWfemfdF6JjgIcGYnq_KohpSHHK6g_oEK-FjwoJd1MdSCp-FMuyhA-feMMZcMb6PeiRUklCu-iicQJFDVdZ-ZBxYL8lgk0YZeGZpPVfn7SyNvfYEpEvPFvEiXb4eor3EZA6OtnWAnsZX89G1P51NbkYXUz9milM_EQKYkiZSklEjI8YTFdq2YTkhwEwSSEtN87I0CoNKAiU5gUgoqiCxlg3Qaafb3H9fg6t0nroYsswsoVg7zYWSQgTyX5AIxpTgtAHPOjAuC-dKSPSqTHNT1ppg3aapW6v6K80GPtmqrqMc7C-6ja8BSAd8pBnUf0jp-4fZ_FvU73ZSV8HmZ8eUi8YOE6F-uZvo6fNozG4vlX5kn_xejqI</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>17339762</pqid></control><display><type>article</type><title>Geometry-based flexible and symmetric protein docking</title><source>MEDLINE</source><source>Wiley Online Library Journals Frontfile Complete</source><creator>Schneidman-Duhovny, Dina ; Inbar, Yuval ; Nussinov, Ruth ; Wolfson, Haim J.</creator><creatorcontrib>Schneidman-Duhovny, Dina ; Inbar, Yuval ; Nussinov, Ruth ; Wolfson, Haim J.</creatorcontrib><description>We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.20562</identifier><identifier>PMID: 15981269</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc., A Wiley Company</publisher><subject>Algorithms ; Animals ; CAPRI ; Computational Biology - methods ; Computer Simulation ; Databases, Protein ; Dimerization ; FlexDock ; flexible docking ; Humans ; Internet ; Macromolecular Substances ; Models, Molecular ; Models, Statistical ; Molecular Conformation ; Mutation ; PatchDock ; Protein Conformation ; Protein Folding ; Protein Interaction Mapping - methods ; Protein Structure, Tertiary ; Proteomics - methods ; Reproducibility of Results ; Software ; Static Electricity ; Structural Homology, Protein ; SymmDock ; symmetric docking ; unbound docking</subject><ispartof>Proteins, structure, function, and bioinformatics, 2005-08, Vol.60 (2), p.224-231</ispartof><rights>Copyright © 2005 Wiley‐Liss, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3962-f77e398ab9832a8b36f95d98abd611e3af48d2a1098a90e9f49861eb7929efdd3</citedby><cites>FETCH-LOGICAL-c3962-f77e398ab9832a8b36f95d98abd611e3af48d2a1098a90e9f49861eb7929efdd3</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.20562$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.20562$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15981269$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schneidman-Duhovny, Dina</creatorcontrib><creatorcontrib>Inbar, Yuval</creatorcontrib><creatorcontrib>Nussinov, Ruth</creatorcontrib><creatorcontrib>Wolfson, Haim J.</creatorcontrib><title>Geometry-based flexible and symmetric protein docking</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.</description><subject>Algorithms</subject><subject>Animals</subject><subject>CAPRI</subject><subject>Computational Biology - methods</subject><subject>Computer Simulation</subject><subject>Databases, Protein</subject><subject>Dimerization</subject><subject>FlexDock</subject><subject>flexible docking</subject><subject>Humans</subject><subject>Internet</subject><subject>Macromolecular Substances</subject><subject>Models, Molecular</subject><subject>Models, Statistical</subject><subject>Molecular Conformation</subject><subject>Mutation</subject><subject>PatchDock</subject><subject>Protein Conformation</subject><subject>Protein Folding</subject><subject>Protein Interaction Mapping - methods</subject><subject>Protein Structure, Tertiary</subject><subject>Proteomics - methods</subject><subject>Reproducibility of Results</subject><subject>Software</subject><subject>Static Electricity</subject><subject>Structural Homology, Protein</subject><subject>SymmDock</subject><subject>symmetric docking</subject><subject>unbound docking</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1Pg0AQhjdGY2v14g8wnDyYUPcD9uNoqq0m1Rqtetws7GCwUCpLY_n3glS96WmSmWfemfdF6JjgIcGYnq_KohpSHHK6g_oEK-FjwoJd1MdSCp-FMuyhA-feMMZcMb6PeiRUklCu-iicQJFDVdZ-ZBxYL8lgk0YZeGZpPVfn7SyNvfYEpEvPFvEiXb4eor3EZA6OtnWAnsZX89G1P51NbkYXUz9milM_EQKYkiZSklEjI8YTFdq2YTkhwEwSSEtN87I0CoNKAiU5gUgoqiCxlg3Qaafb3H9fg6t0nroYsswsoVg7zYWSQgTyX5AIxpTgtAHPOjAuC-dKSPSqTHNT1ppg3aapW6v6K80GPtmqrqMc7C-6ja8BSAd8pBnUf0jp-4fZ_FvU73ZSV8HmZ8eUi8YOE6F-uZvo6fNozG4vlX5kn_xejqI</recordid><startdate>20050801</startdate><enddate>20050801</enddate><creator>Schneidman-Duhovny, Dina</creator><creator>Inbar, Yuval</creator><creator>Nussinov, Ruth</creator><creator>Wolfson, Haim J.</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>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20050801</creationdate><title>Geometry-based flexible and symmetric protein docking</title><author>Schneidman-Duhovny, Dina ; Inbar, Yuval ; Nussinov, Ruth ; Wolfson, Haim J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3962-f77e398ab9832a8b36f95d98abd611e3af48d2a1098a90e9f49861eb7929efdd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>CAPRI</topic><topic>Computational Biology - methods</topic><topic>Computer Simulation</topic><topic>Databases, Protein</topic><topic>Dimerization</topic><topic>FlexDock</topic><topic>flexible docking</topic><topic>Humans</topic><topic>Internet</topic><topic>Macromolecular Substances</topic><topic>Models, Molecular</topic><topic>Models, Statistical</topic><topic>Molecular Conformation</topic><topic>Mutation</topic><topic>PatchDock</topic><topic>Protein Conformation</topic><topic>Protein Folding</topic><topic>Protein Interaction Mapping - methods</topic><topic>Protein Structure, Tertiary</topic><topic>Proteomics - methods</topic><topic>Reproducibility of Results</topic><topic>Software</topic><topic>Static Electricity</topic><topic>Structural Homology, Protein</topic><topic>SymmDock</topic><topic>symmetric docking</topic><topic>unbound docking</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schneidman-Duhovny, Dina</creatorcontrib><creatorcontrib>Inbar, Yuval</creatorcontrib><creatorcontrib>Nussinov, Ruth</creatorcontrib><creatorcontrib>Wolfson, Haim J.</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>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schneidman-Duhovny, Dina</au><au>Inbar, Yuval</au><au>Nussinov, Ruth</au><au>Wolfson, Haim J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Geometry-based flexible and symmetric protein docking</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2005-08-01</date><risdate>2005</risdate><volume>60</volume><issue>2</issue><spage>224</spage><epage>231</epage><pages>224-231</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.</abstract><cop>Hoboken</cop><pub>Wiley Subscription Services, Inc., A Wiley Company</pub><pmid>15981269</pmid><doi>10.1002/prot.20562</doi><tpages>8</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0887-3585 |
| ispartof | Proteins, structure, function, and bioinformatics, 2005-08, Vol.60 (2), p.224-231 |
| issn | 0887-3585 1097-0134 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_67987748 |
| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Algorithms Animals CAPRI Computational Biology - methods Computer Simulation Databases, Protein Dimerization FlexDock flexible docking Humans Internet Macromolecular Substances Models, Molecular Models, Statistical Molecular Conformation Mutation PatchDock Protein Conformation Protein Folding Protein Interaction Mapping - methods Protein Structure, Tertiary Proteomics - methods Reproducibility of Results Software Static Electricity Structural Homology, Protein SymmDock symmetric docking unbound docking |
| title | Geometry-based flexible and symmetric protein docking |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T01%3A46%3A13IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Geometry-based%20flexible%20and%20symmetric%20protein%20docking&rft.jtitle=Proteins,%20structure,%20function,%20and%20bioinformatics&rft.au=Schneidman-Duhovny,%20Dina&rft.date=2005-08-01&rft.volume=60&rft.issue=2&rft.spage=224&rft.epage=231&rft.pages=224-231&rft.issn=0887-3585&rft.eissn=1097-0134&rft_id=info:doi/10.1002/prot.20562&rft_dat=%3Cproquest_cross%3E17339762%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=17339762&rft_id=info:pmid/15981269&rfr_iscdi=true |