The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite
The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To...
Gespeichert in:
| Veröffentlicht in: | PloS one 2013-07, Vol.8 (7), p.e66856-e66856 |
|---|---|
| Hauptverfasser: | , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e66856 |
|---|---|
| container_issue | 7 |
| container_start_page | e66856 |
| container_title | PloS one |
| container_volume | 8 |
| creator | Adolf-Bryfogle, Jared Dunbrack, Jr, Roland L |
| description | The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI. |
| doi_str_mv | 10.1371/journal.pone.0066856 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1974582222</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A478358035</galeid><doaj_id>oai_doaj_org_article_1c743ce9fea64963bdb69753e7c65822</doaj_id><sourcerecordid>A478358035</sourcerecordid><originalsourceid>FETCH-LOGICAL-c758t-d586a393f0511c36d1f3f8dcdd2390a8f0fac80ec787c708ae34a51714c058753</originalsourceid><addsrcrecordid>eNqNkl1v0zAYhSMEYmPwDxBEQkJw0WLXju1wgTRNfFSatGkUbi3Xed16uHFnO8D-PQ5NpwbtguQikfOcc-w3pyieYzTFhON3174LrXLTrW9hihBjomIPimNck9mEzRB5ePB-VDyJ8RqhigjGHhdHMyI4pQgdF5eLNZSXt1c-QkqqXHjvftj0vlTlKqjt2mrlyi5CKG2bIBiloTQ-lCmr9proTfqlApSxswmeFo-MchGeDc-T4tunj4uzL5Pzi8_zs9PzieaVSJOmEkyRmhhUYawJa7AhRjS6aWakRkoYlLMEAs0F1xwJBYSqCnNMNaoEr8hJ8XLnu3U-ymEYUeKa00rM8pWJ-Y5ovLqW22A3KtxKr6z8u-DDSqqQrHYgseaUaKgNKEZrRpbNktU5BLhmvVv2-jCkdcsNNBraFJQbmY6_tHYtV_6nJBwxKlA2eDMYBH_TQUxyY6MG51QLvsv7phgzkrfdo6_-Qe8_3UCtVD6AbY3Pubo3laeUC1Ll0H5K03uofDewsTo3x9i8PhK8HQkyk-B3WqkuRjn_evX_7MX3Mfv6gF2DcmkdveuS9W0cg3QH6uBjDGDuhoyR7Iu_n4bsiy-H4mfZi8MfdCfaN538ASlM_G4</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1974582222</pqid></control><display><type>article</type><title>The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS) Journals Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Adolf-Bryfogle, Jared ; Dunbrack, Jr, Roland L</creator><contributor>Sticht, Heinrich</contributor><creatorcontrib>Adolf-Bryfogle, Jared ; Dunbrack, Jr, Roland L ; Sticht, Heinrich</creatorcontrib><description>The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0066856</identifier><identifier>PMID: 23874400</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology ; C plus plus ; Cancer ; Computational Biology - methods ; Computer applications ; Computer Science ; Documentation ; Engineering ; Graphical user interface ; Humans ; International economic relations ; Internet ; Medical research ; Models, Molecular ; Molecular modelling ; Proteins ; Software ; Software industry ; Software packages ; User interface ; User-Computer Interface</subject><ispartof>PloS one, 2013-07, Vol.8 (7), p.e66856-e66856</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Adolf-Bryfogle, Dunbrack. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Adolf-Bryfogle, Dunbrack 2013 Adolf-Bryfogle, Dunbrack</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-d586a393f0511c36d1f3f8dcdd2390a8f0fac80ec787c708ae34a51714c058753</citedby><cites>FETCH-LOGICAL-c758t-d586a393f0511c36d1f3f8dcdd2390a8f0fac80ec787c708ae34a51714c058753</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706480/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706480/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23871,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23874400$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Sticht, Heinrich</contributor><creatorcontrib>Adolf-Bryfogle, Jared</creatorcontrib><creatorcontrib>Dunbrack, Jr, Roland L</creatorcontrib><title>The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.</description><subject>Biology</subject><subject>C plus plus</subject><subject>Cancer</subject><subject>Computational Biology - methods</subject><subject>Computer applications</subject><subject>Computer Science</subject><subject>Documentation</subject><subject>Engineering</subject><subject>Graphical user interface</subject><subject>Humans</subject><subject>International economic relations</subject><subject>Internet</subject><subject>Medical research</subject><subject>Models, Molecular</subject><subject>Molecular modelling</subject><subject>Proteins</subject><subject>Software</subject><subject>Software industry</subject><subject>Software packages</subject><subject>User interface</subject><subject>User-Computer Interface</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl1v0zAYhSMEYmPwDxBEQkJw0WLXju1wgTRNfFSatGkUbi3Xed16uHFnO8D-PQ5NpwbtguQikfOcc-w3pyieYzTFhON3174LrXLTrW9hihBjomIPimNck9mEzRB5ePB-VDyJ8RqhigjGHhdHMyI4pQgdF5eLNZSXt1c-QkqqXHjvftj0vlTlKqjt2mrlyi5CKG2bIBiloTQ-lCmr9proTfqlApSxswmeFo-MchGeDc-T4tunj4uzL5Pzi8_zs9PzieaVSJOmEkyRmhhUYawJa7AhRjS6aWakRkoYlLMEAs0F1xwJBYSqCnNMNaoEr8hJ8XLnu3U-ymEYUeKa00rM8pWJ-Y5ovLqW22A3KtxKr6z8u-DDSqqQrHYgseaUaKgNKEZrRpbNktU5BLhmvVv2-jCkdcsNNBraFJQbmY6_tHYtV_6nJBwxKlA2eDMYBH_TQUxyY6MG51QLvsv7phgzkrfdo6_-Qe8_3UCtVD6AbY3Pubo3laeUC1Ll0H5K03uofDewsTo3x9i8PhK8HQkyk-B3WqkuRjn_evX_7MX3Mfv6gF2DcmkdveuS9W0cg3QH6uBjDGDuhoyR7Iu_n4bsiy-H4mfZi8MfdCfaN538ASlM_G4</recordid><startdate>20130709</startdate><enddate>20130709</enddate><creator>Adolf-Bryfogle, Jared</creator><creator>Dunbrack, Jr, Roland L</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130709</creationdate><title>The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite</title><author>Adolf-Bryfogle, Jared ; Dunbrack, Jr, Roland L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-d586a393f0511c36d1f3f8dcdd2390a8f0fac80ec787c708ae34a51714c058753</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Biology</topic><topic>C plus plus</topic><topic>Cancer</topic><topic>Computational Biology - methods</topic><topic>Computer applications</topic><topic>Computer Science</topic><topic>Documentation</topic><topic>Engineering</topic><topic>Graphical user interface</topic><topic>Humans</topic><topic>International economic relations</topic><topic>Internet</topic><topic>Medical research</topic><topic>Models, Molecular</topic><topic>Molecular modelling</topic><topic>Proteins</topic><topic>Software</topic><topic>Software industry</topic><topic>Software packages</topic><topic>User interface</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Adolf-Bryfogle, Jared</creatorcontrib><creatorcontrib>Dunbrack, Jr, Roland L</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection (ProQuest)</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Adolf-Bryfogle, Jared</au><au>Dunbrack, Jr, Roland L</au><au>Sticht, Heinrich</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-07-09</date><risdate>2013</risdate><volume>8</volume><issue>7</issue><spage>e66856</spage><epage>e66856</epage><pages>e66856-e66856</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23874400</pmid><doi>10.1371/journal.pone.0066856</doi><tpages>e66856</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-07, Vol.8 (7), p.e66856-e66856 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1974582222 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Biology C plus plus Cancer Computational Biology - methods Computer applications Computer Science Documentation Engineering Graphical user interface Humans International economic relations Internet Medical research Models, Molecular Molecular modelling Proteins Software Software industry Software packages User interface User-Computer Interface |
| title | The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-13T07%3A54%3A04IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20PyRosetta%20Toolkit:%20a%20graphical%20user%20interface%20for%20the%20Rosetta%20software%20suite&rft.jtitle=PloS%20one&rft.au=Adolf-Bryfogle,%20Jared&rft.date=2013-07-09&rft.volume=8&rft.issue=7&rft.spage=e66856&rft.epage=e66856&rft.pages=e66856-e66856&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0066856&rft_dat=%3Cgale_plos_%3EA478358035%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1974582222&rft_id=info:pmid/23874400&rft_galeid=A478358035&rft_doaj_id=oai_doaj_org_article_1c743ce9fea64963bdb69753e7c65822&rfr_iscdi=true |