UDock2: interactive real-time multi-body protein–protein docking software
Abstract Motivation Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to a...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2022-01, Vol.39 (10) |
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| container_title | Bioinformatics (Oxford, England) |
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| creator | Plateau-Holleville, Cyprien Guionnière, Simon Boyer, Benjamin Jiménez-Garcia, Brian Levieux, Guillaume Mérillou, Stéphane Maria, Maxime Montes, Matthieu |
| description | Abstract
Motivation
Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software.
Results
This article presents an interactive multi-body protein–protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties.
Availability and implementation
UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2. |
| doi_str_mv | 10.1093/bioinformatics/btad609 |
| format | Article |
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Motivation
Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software.
Results
This article presents an interactive multi-body protein–protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties.
Availability and implementation
UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.</description><identifier>ISSN: 1367-4811</identifier><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btad609</identifier><identifier>PMID: 37792496</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Note ; Biochemistry, Molecular Biology ; Bioinformatics ; Computer Science ; Life Sciences ; Structural Biology</subject><ispartof>Bioinformatics (Oxford, England), 2022-01, Vol.39 (10)</ispartof><rights>The Author(s) 2023. Published by Oxford University Press. 2023</rights><rights>The Author(s) 2023. Published by Oxford University Press.</rights><rights>Attribution</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c491t-11c3930f37f6e78429d33daad0965d0290c58fdf7d3e132048dcf85c5956250c3</citedby><cites>FETCH-LOGICAL-c491t-11c3930f37f6e78429d33daad0965d0290c58fdf7d3e132048dcf85c5956250c3</cites><orcidid>0000-0001-5921-460X ; 0000-0003-1510-557X ; 0000-0003-2820-8076</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10938049/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10938049/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,1599,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37792496$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04356674$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Ponty, Yann</contributor><creatorcontrib>Plateau-Holleville, Cyprien</creatorcontrib><creatorcontrib>Guionnière, Simon</creatorcontrib><creatorcontrib>Boyer, Benjamin</creatorcontrib><creatorcontrib>Jiménez-Garcia, Brian</creatorcontrib><creatorcontrib>Levieux, Guillaume</creatorcontrib><creatorcontrib>Mérillou, Stéphane</creatorcontrib><creatorcontrib>Maria, Maxime</creatorcontrib><creatorcontrib>Montes, Matthieu</creatorcontrib><title>UDock2: interactive real-time multi-body protein–protein docking software</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software.
Results
This article presents an interactive multi-body protein–protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties.
Availability and implementation
UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.</description><subject>Applications Note</subject><subject>Biochemistry, Molecular Biology</subject><subject>Bioinformatics</subject><subject>Computer Science</subject><subject>Life Sciences</subject><subject>Structural Biology</subject><issn>1367-4811</issn><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNqNkctOwzAQRS0E4v0LVZawCPUjdmI2CPEqohIbWFuuH9SQxMV2itjxD_whX0KgBQErVh55zr2jmQvAAMEDBDkZTpx3rfWhkcmpOJwkqRnkK2ATEVbmRYXQ6o96A2zFeA8hpJCydbBBypLjgrNNcHV76tUDPsxcm0yQKrm5yYKRdZ5cY7Kmq5PLJ14_Z7Pgk3Ht28vrssp0r3TtXRa9TU8ymB2wZmUdze7y3Qa352c3J6N8fH1xeXI8zlXBUcoRUoQTaElpmSmrAnNNiJZSQ86ohphDRSurbamJQQTDotLKVlRRThmmUJFtcLTwnXWTxmhl2hRkLWbBNTI8Cy-d-N1p3VTc-bn4uFwFC9477C8cpn90o-Ox-PiDBaGMlcUc9ezeclrwj52JSTQuKlPXsjW-iwJXJcG0vybuUbZAVfAxBmO_vRH8HC5-xyaWsfXCwc-NvmVfOfUAWgC-m_3X9B1mtazR</recordid><startdate>20220101</startdate><enddate>20220101</enddate><creator>Plateau-Holleville, Cyprien</creator><creator>Guionnière, Simon</creator><creator>Boyer, Benjamin</creator><creator>Jiménez-Garcia, Brian</creator><creator>Levieux, Guillaume</creator><creator>Mérillou, Stéphane</creator><creator>Maria, Maxime</creator><creator>Montes, Matthieu</creator><general>Oxford University Press</general><general>Oxford University Press (OUP)</general><scope>TOX</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5921-460X</orcidid><orcidid>https://orcid.org/0000-0003-1510-557X</orcidid><orcidid>https://orcid.org/0000-0003-2820-8076</orcidid></search><sort><creationdate>20220101</creationdate><title>UDock2: interactive real-time multi-body protein–protein docking software</title><author>Plateau-Holleville, Cyprien ; Guionnière, Simon ; Boyer, Benjamin ; Jiménez-Garcia, Brian ; Levieux, Guillaume ; Mérillou, Stéphane ; Maria, Maxime ; Montes, Matthieu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c491t-11c3930f37f6e78429d33daad0965d0290c58fdf7d3e132048dcf85c5956250c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Applications Note</topic><topic>Biochemistry, Molecular Biology</topic><topic>Bioinformatics</topic><topic>Computer Science</topic><topic>Life Sciences</topic><topic>Structural Biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Plateau-Holleville, Cyprien</creatorcontrib><creatorcontrib>Guionnière, Simon</creatorcontrib><creatorcontrib>Boyer, Benjamin</creatorcontrib><creatorcontrib>Jiménez-Garcia, Brian</creatorcontrib><creatorcontrib>Levieux, Guillaume</creatorcontrib><creatorcontrib>Mérillou, Stéphane</creatorcontrib><creatorcontrib>Maria, Maxime</creatorcontrib><creatorcontrib>Montes, Matthieu</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Plateau-Holleville, Cyprien</au><au>Guionnière, Simon</au><au>Boyer, Benjamin</au><au>Jiménez-Garcia, Brian</au><au>Levieux, Guillaume</au><au>Mérillou, Stéphane</au><au>Maria, Maxime</au><au>Montes, Matthieu</au><au>Ponty, Yann</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>UDock2: interactive real-time multi-body protein–protein docking software</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2022-01-01</date><risdate>2022</risdate><volume>39</volume><issue>10</issue><issn>1367-4811</issn><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
Protein–protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software.
Results
This article presents an interactive multi-body protein–protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties.
Availability and implementation
UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37792496</pmid><doi>10.1093/bioinformatics/btad609</doi><orcidid>https://orcid.org/0000-0001-5921-460X</orcidid><orcidid>https://orcid.org/0000-0003-1510-557X</orcidid><orcidid>https://orcid.org/0000-0003-2820-8076</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics (Oxford, England), 2022-01, Vol.39 (10) |
| issn | 1367-4811 1367-4803 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Note Biochemistry, Molecular Biology Bioinformatics Computer Science Life Sciences Structural Biology |
| title | UDock2: interactive real-time multi-body protein–protein docking software |
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