OpenStructure: an integrated software framework for computational structural biology

Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructu...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2013-05, Vol.69 (5), p.701-709
Hauptverfasser: Biasini, M., Schmidt, T., Bienert, S., Mariani, V., Studer, G., Haas, J., Johner, N., Schenk, A. D., Philippsen, A., Schwede, T.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 709
container_issue 5
container_start_page 701
container_title Acta crystallographica. Section D, Biological crystallography.
container_volume 69
creator Biasini, M.
Schmidt, T.
Bienert, S.
Mariani, V.
Studer, G.
Haas, J.
Johner, N.
Schenk, A. D.
Philippsen, A.
Schwede, T.
description Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular‐structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.
doi_str_mv 10.1107/S0907444913007051
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3640466</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2958467451</sourcerecordid><originalsourceid>FETCH-LOGICAL-c5470-2d5aa533f0de4a7bb0d124f7305e2a4719a855baf4dfb9b48708329259f5d8843</originalsourceid><addsrcrecordid>eNqFkU1v1DAQhi0Eoh_wA7igSFy4BMZfmYQDUrWFUrSihxZVnCwnsZe0SbzYDtv99xhlWRU49OSR_bzvjOcl5AWFN5QCvr2EClAIUVEOgCDpI3JIeVXlAAIf36sPyFEINwDAGMen5IDxgnOJ1SG5ulib8TL6qYmTN-8yPWbdGM3K62jaLDgbN9qbzHo9mI3zt5l1PmvcsJ6ijp0bdZ-FnTqVded6t9o-I0-s7oN5vjuPydePH64Wn_Llxdn54mSZN1Ig5KyVWkvOLbRGaKxraCkTFjlIw7RAWulSylpb0dq6qkWJUHJWMVlZ2Zal4Mfk_ey7nurBtI0ZY5pCrX03aL9VTnfq75ex-65W7qfihQBRFMng9c7Aux-TCVENXWhM3-vRuCkoygtJhSjTgh9GBWKJiJDQV_-gN27yaVUzxQoKHBNFZ6rxLgRv7H5uCup3vOq_eJPm5f0P7xV_8kxAOQObrjfbhx3VybfT84VM10maz9IuRHO3l2p_qwrkKNX1lzNVnl7TzwVfpo6_AAbCv5w</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1347261037</pqid></control><display><type>article</type><title>OpenStructure: an integrated software framework for computational structural biology</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><source>Alma/SFX Local Collection</source><creator>Biasini, M. ; Schmidt, T. ; Bienert, S. ; Mariani, V. ; Studer, G. ; Haas, J. ; Johner, N. ; Schenk, A. D. ; Philippsen, A. ; Schwede, T.</creator><creatorcontrib>Biasini, M. ; Schmidt, T. ; Bienert, S. ; Mariani, V. ; Studer, G. ; Haas, J. ; Johner, N. ; Schenk, A. D. ; Philippsen, A. ; Schwede, T.</creatorcontrib><description>Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular‐structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.</description><identifier>ISSN: 1399-0047</identifier><identifier>ISSN: 0907-4449</identifier><identifier>EISSN: 1399-0047</identifier><identifier>DOI: 10.1107/S0907444913007051</identifier><identifier>PMID: 23633579</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography</publisher><subject>Algorithms ; Biology ; Computational Biology - methods ; computational structural biology ; Computer programs ; Dengue Virus - enzymology ; Density ; Evolutionary ; Integrated software ; Integrative Structural Biology ; Licenses ; Methyltransferases - chemistry ; Molecular Structure ; OpenStructure ; Programming Languages ; Proteomics - methods ; Sequence Alignment ; Software ; Three dimensional ; Urease - chemistry ; User-Computer Interface</subject><ispartof>Acta crystallographica. Section D, Biological crystallography., 2013-05, Vol.69 (5), p.701-709</ispartof><rights>Biasini et al. 2013</rights><rights>Biasini et al. 2013</rights><rights>Biasini et al. 2013 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5470-2d5aa533f0de4a7bb0d124f7305e2a4719a855baf4dfb9b48708329259f5d8843</citedby><cites>FETCH-LOGICAL-c5470-2d5aa533f0de4a7bb0d124f7305e2a4719a855baf4dfb9b48708329259f5d8843</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1107%2FS0907444913007051$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1107%2FS0907444913007051$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,315,782,786,887,1419,27931,27932,45581,45582</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23633579$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Biasini, M.</creatorcontrib><creatorcontrib>Schmidt, T.</creatorcontrib><creatorcontrib>Bienert, S.</creatorcontrib><creatorcontrib>Mariani, V.</creatorcontrib><creatorcontrib>Studer, G.</creatorcontrib><creatorcontrib>Haas, J.</creatorcontrib><creatorcontrib>Johner, N.</creatorcontrib><creatorcontrib>Schenk, A. D.</creatorcontrib><creatorcontrib>Philippsen, A.</creatorcontrib><creatorcontrib>Schwede, T.</creatorcontrib><title>OpenStructure: an integrated software framework for computational structural biology</title><title>Acta crystallographica. Section D, Biological crystallography.</title><addtitle>Acta Cryst. D</addtitle><description>Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular‐structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.</description><subject>Algorithms</subject><subject>Biology</subject><subject>Computational Biology - methods</subject><subject>computational structural biology</subject><subject>Computer programs</subject><subject>Dengue Virus - enzymology</subject><subject>Density</subject><subject>Evolutionary</subject><subject>Integrated software</subject><subject>Integrative Structural Biology</subject><subject>Licenses</subject><subject>Methyltransferases - chemistry</subject><subject>Molecular Structure</subject><subject>OpenStructure</subject><subject>Programming Languages</subject><subject>Proteomics - methods</subject><subject>Sequence Alignment</subject><subject>Software</subject><subject>Three dimensional</subject><subject>Urease - chemistry</subject><subject>User-Computer Interface</subject><issn>1399-0047</issn><issn>0907-4449</issn><issn>1399-0047</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhi0Eoh_wA7igSFy4BMZfmYQDUrWFUrSihxZVnCwnsZe0SbzYDtv99xhlWRU49OSR_bzvjOcl5AWFN5QCvr2EClAIUVEOgCDpI3JIeVXlAAIf36sPyFEINwDAGMen5IDxgnOJ1SG5ulib8TL6qYmTN-8yPWbdGM3K62jaLDgbN9qbzHo9mI3zt5l1PmvcsJ6ijp0bdZ-FnTqVded6t9o-I0-s7oN5vjuPydePH64Wn_Llxdn54mSZN1Ig5KyVWkvOLbRGaKxraCkTFjlIw7RAWulSylpb0dq6qkWJUHJWMVlZ2Zal4Mfk_ey7nurBtI0ZY5pCrX03aL9VTnfq75ex-65W7qfihQBRFMng9c7Aux-TCVENXWhM3-vRuCkoygtJhSjTgh9GBWKJiJDQV_-gN27yaVUzxQoKHBNFZ6rxLgRv7H5uCup3vOq_eJPm5f0P7xV_8kxAOQObrjfbhx3VybfT84VM10maz9IuRHO3l2p_qwrkKNX1lzNVnl7TzwVfpo6_AAbCv5w</recordid><startdate>201305</startdate><enddate>201305</enddate><creator>Biasini, M.</creator><creator>Schmidt, T.</creator><creator>Bienert, S.</creator><creator>Mariani, V.</creator><creator>Studer, G.</creator><creator>Haas, J.</creator><creator>Johner, N.</creator><creator>Schenk, A. D.</creator><creator>Philippsen, A.</creator><creator>Schwede, T.</creator><general>International Union of Crystallography</general><general>Wiley Subscription Services, Inc</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>7QP</scope><scope>7SP</scope><scope>7SR</scope><scope>7TK</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>H8D</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201305</creationdate><title>OpenStructure: an integrated software framework for computational structural biology</title><author>Biasini, M. ; Schmidt, T. ; Bienert, S. ; Mariani, V. ; Studer, G. ; Haas, J. ; Johner, N. ; Schenk, A. D. ; Philippsen, A. ; Schwede, T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5470-2d5aa533f0de4a7bb0d124f7305e2a4719a855baf4dfb9b48708329259f5d8843</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Algorithms</topic><topic>Biology</topic><topic>Computational Biology - methods</topic><topic>computational structural biology</topic><topic>Computer programs</topic><topic>Dengue Virus - enzymology</topic><topic>Density</topic><topic>Evolutionary</topic><topic>Integrated software</topic><topic>Integrative Structural Biology</topic><topic>Licenses</topic><topic>Methyltransferases - chemistry</topic><topic>Molecular Structure</topic><topic>OpenStructure</topic><topic>Programming Languages</topic><topic>Proteomics - methods</topic><topic>Sequence Alignment</topic><topic>Software</topic><topic>Three dimensional</topic><topic>Urease - chemistry</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Biasini, M.</creatorcontrib><creatorcontrib>Schmidt, T.</creatorcontrib><creatorcontrib>Bienert, S.</creatorcontrib><creatorcontrib>Mariani, V.</creatorcontrib><creatorcontrib>Studer, G.</creatorcontrib><creatorcontrib>Haas, J.</creatorcontrib><creatorcontrib>Johner, N.</creatorcontrib><creatorcontrib>Schenk, A. D.</creatorcontrib><creatorcontrib>Philippsen, A.</creatorcontrib><creatorcontrib>Schwede, T.</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>Calcium &amp; Calcified Tissue Abstracts</collection><collection>Electronics &amp; Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Biasini, M.</au><au>Schmidt, T.</au><au>Bienert, S.</au><au>Mariani, V.</au><au>Studer, G.</au><au>Haas, J.</au><au>Johner, N.</au><au>Schenk, A. D.</au><au>Philippsen, A.</au><au>Schwede, T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>OpenStructure: an integrated software framework for computational structural biology</atitle><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle><addtitle>Acta Cryst. D</addtitle><date>2013-05</date><risdate>2013</risdate><volume>69</volume><issue>5</issue><spage>701</spage><epage>709</epage><pages>701-709</pages><issn>1399-0047</issn><issn>0907-4449</issn><eissn>1399-0047</eissn><abstract>Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular‐structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><pmid>23633579</pmid><doi>10.1107/S0907444913007051</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1399-0047
ispartof Acta crystallographica. Section D, Biological crystallography., 2013-05, Vol.69 (5), p.701-709
issn 1399-0047
0907-4449
1399-0047
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3640466
source MEDLINE; Access via Wiley Online Library; Alma/SFX Local Collection
subjects Algorithms
Biology
Computational Biology - methods
computational structural biology
Computer programs
Dengue Virus - enzymology
Density
Evolutionary
Integrated software
Integrative Structural Biology
Licenses
Methyltransferases - chemistry
Molecular Structure
OpenStructure
Programming Languages
Proteomics - methods
Sequence Alignment
Software
Three dimensional
Urease - chemistry
User-Computer Interface
title OpenStructure: an integrated software framework for computational structural biology
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-05T16%3A18%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=OpenStructure:%20an%20integrated%20software%20framework%20for%20computational%20structural%20biology&rft.jtitle=Acta%20crystallographica.%20Section%20D,%20Biological%20crystallography.&rft.au=Biasini,%20M.&rft.date=2013-05&rft.volume=69&rft.issue=5&rft.spage=701&rft.epage=709&rft.pages=701-709&rft.issn=1399-0047&rft.eissn=1399-0047&rft_id=info:doi/10.1107/S0907444913007051&rft_dat=%3Cproquest_pubme%3E2958467451%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1347261037&rft_id=info:pmid/23633579&rfr_iscdi=true