IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nucleic acids research 2012-01, Vol.40 (D1), p.D834-D840
Hauptverfasser: Shoemaker, Benjamin A., Zhang, Dachuan, Tyagi, Manoj, Thangudu, Ratna R., Fong, Jessica H., Marchler-Bauer, Aron, Bryant, Stephen H., Madej, Thomas, Panchenko, Anna R.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page D840
container_issue D1
container_start_page D834
container_title Nucleic acids research
container_volume 40
creator Shoemaker, Benjamin A.
Zhang, Dachuan
Tyagi, Manoj
Thangudu, Ratna R.
Fong, Jessica H.
Marchler-Bauer, Aron
Bryant, Stephen H.
Madej, Thomas
Panchenko, Anna R.
description We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.
doi_str_mv 10.1093/nar/gkr997
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3245142</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkr997</oup_id><sourcerecordid>912642787</sourcerecordid><originalsourceid>FETCH-LOGICAL-c505t-d9e540d71aa309ef55d47d537c6b0ada29fbbcb3cabe7345c76985599347caae3</originalsourceid><addsrcrecordid>eNqFkc1u1TAQRi0EoreFDQ-AvEGUilD_xtcbJFrRNlIlFoW15TiTiyGxg-1U6gvw3KTKpYINrEajOXM0ow-hF5S8o0Tz02DT6e570lo9QhvKa1YJXbPHaEM4kRUlYnuADnP-RggVVIqn6IAxSpjUdIN-NmfNDT5uQg8pQYfPfBzjAG4ebMJNKJCsKz4GfAPpFtIbnGCKqeS3eFpw70rGNnTYL-Qu2QIZj_NQ_DQALnfT0sYeuxjy_faK7YUZ9zEtkljAh_wMPentkOH5vh6hLxcfP59fVdefLpvzD9eVk0SWqtMgBekUtZYTDb2UnVCd5MrVLbGdZbpvW9dyZ1tQXEinar2VUmsulLMW-BF6v3qnuR2hcxBKsoOZkh9tujPRevP3JPivZhdvDWdCUsEWweu9IMUfM-RiRp8dDIMNEOdsNCNKi60m_ycpqwVTW7WQJyvpUsw5Qf9wDyXmPmGzJGzWhBf45Z8fPKC_I12AVysQ5-lfol8vwrPR</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>912642787</pqid></control><display><type>article</type><title>IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins</title><source>OUP_牛津大学出版社OA刊</source><source>MEDLINE</source><source>Directory of Open Access Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Shoemaker, Benjamin A. ; Zhang, Dachuan ; Tyagi, Manoj ; Thangudu, Ratna R. ; Fong, Jessica H. ; Marchler-Bauer, Aron ; Bryant, Stephen H. ; Madej, Thomas ; Panchenko, Anna R.</creator><creatorcontrib>Shoemaker, Benjamin A. ; Zhang, Dachuan ; Tyagi, Manoj ; Thangudu, Ratna R. ; Fong, Jessica H. ; Marchler-Bauer, Aron ; Bryant, Stephen H. ; Madej, Thomas ; Panchenko, Anna R.</creatorcontrib><description>We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkr997</identifier><identifier>PMID: 22102591</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Binding Sites ; Computer Graphics ; Databases, Protein ; Ions - chemistry ; Molecular Sequence Annotation ; Multiprotein Complexes - chemistry ; Nucleic Acids - chemistry ; Peptides - chemistry ; Protein Interaction Mapping ; Proteins - chemistry ; Sequence Analysis, Protein ; Systems Integration ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2012-01, Vol.40 (D1), p.D834-D840</ispartof><rights>Published by Oxford University Press 2011. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c505t-d9e540d71aa309ef55d47d537c6b0ada29fbbcb3cabe7345c76985599347caae3</citedby><cites>FETCH-LOGICAL-c505t-d9e540d71aa309ef55d47d537c6b0ada29fbbcb3cabe7345c76985599347caae3</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/PMC3245142/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245142/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22102591$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shoemaker, Benjamin A.</creatorcontrib><creatorcontrib>Zhang, Dachuan</creatorcontrib><creatorcontrib>Tyagi, Manoj</creatorcontrib><creatorcontrib>Thangudu, Ratna R.</creatorcontrib><creatorcontrib>Fong, Jessica H.</creatorcontrib><creatorcontrib>Marchler-Bauer, Aron</creatorcontrib><creatorcontrib>Bryant, Stephen H.</creatorcontrib><creatorcontrib>Madej, Thomas</creatorcontrib><creatorcontrib>Panchenko, Anna R.</creatorcontrib><title>IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.</description><subject>Binding Sites</subject><subject>Computer Graphics</subject><subject>Databases, Protein</subject><subject>Ions - chemistry</subject><subject>Molecular Sequence Annotation</subject><subject>Multiprotein Complexes - chemistry</subject><subject>Nucleic Acids - chemistry</subject><subject>Peptides - chemistry</subject><subject>Protein Interaction Mapping</subject><subject>Proteins - chemistry</subject><subject>Sequence Analysis, Protein</subject><subject>Systems Integration</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqFkc1u1TAQRi0EoreFDQ-AvEGUilD_xtcbJFrRNlIlFoW15TiTiyGxg-1U6gvw3KTKpYINrEajOXM0ow-hF5S8o0Tz02DT6e570lo9QhvKa1YJXbPHaEM4kRUlYnuADnP-RggVVIqn6IAxSpjUdIN-NmfNDT5uQg8pQYfPfBzjAG4ebMJNKJCsKz4GfAPpFtIbnGCKqeS3eFpw70rGNnTYL-Qu2QIZj_NQ_DQALnfT0sYeuxjy_faK7YUZ9zEtkljAh_wMPentkOH5vh6hLxcfP59fVdefLpvzD9eVk0SWqtMgBekUtZYTDb2UnVCd5MrVLbGdZbpvW9dyZ1tQXEinar2VUmsulLMW-BF6v3qnuR2hcxBKsoOZkh9tujPRevP3JPivZhdvDWdCUsEWweu9IMUfM-RiRp8dDIMNEOdsNCNKi60m_ycpqwVTW7WQJyvpUsw5Qf9wDyXmPmGzJGzWhBf45Z8fPKC_I12AVysQ5-lfol8vwrPR</recordid><startdate>20120101</startdate><enddate>20120101</enddate><creator>Shoemaker, Benjamin A.</creator><creator>Zhang, Dachuan</creator><creator>Tyagi, Manoj</creator><creator>Thangudu, Ratna R.</creator><creator>Fong, Jessica H.</creator><creator>Marchler-Bauer, Aron</creator><creator>Bryant, Stephen H.</creator><creator>Madej, Thomas</creator><creator>Panchenko, Anna R.</creator><general>Oxford University Press</general><scope>TOX</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><scope>7ST</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>5PM</scope></search><sort><creationdate>20120101</creationdate><title>IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins</title><author>Shoemaker, Benjamin A. ; Zhang, Dachuan ; Tyagi, Manoj ; Thangudu, Ratna R. ; Fong, Jessica H. ; Marchler-Bauer, Aron ; Bryant, Stephen H. ; Madej, Thomas ; Panchenko, Anna R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c505t-d9e540d71aa309ef55d47d537c6b0ada29fbbcb3cabe7345c76985599347caae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Binding Sites</topic><topic>Computer Graphics</topic><topic>Databases, Protein</topic><topic>Ions - chemistry</topic><topic>Molecular Sequence Annotation</topic><topic>Multiprotein Complexes - chemistry</topic><topic>Nucleic Acids - chemistry</topic><topic>Peptides - chemistry</topic><topic>Protein Interaction Mapping</topic><topic>Proteins - chemistry</topic><topic>Sequence Analysis, Protein</topic><topic>Systems Integration</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shoemaker, Benjamin A.</creatorcontrib><creatorcontrib>Zhang, Dachuan</creatorcontrib><creatorcontrib>Tyagi, Manoj</creatorcontrib><creatorcontrib>Thangudu, Ratna R.</creatorcontrib><creatorcontrib>Fong, Jessica H.</creatorcontrib><creatorcontrib>Marchler-Bauer, Aron</creatorcontrib><creatorcontrib>Bryant, Stephen H.</creatorcontrib><creatorcontrib>Madej, Thomas</creatorcontrib><creatorcontrib>Panchenko, Anna R.</creatorcontrib><collection>OUP_牛津大学出版社OA刊</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Environment Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shoemaker, Benjamin A.</au><au>Zhang, Dachuan</au><au>Tyagi, Manoj</au><au>Thangudu, Ratna R.</au><au>Fong, Jessica H.</au><au>Marchler-Bauer, Aron</au><au>Bryant, Stephen H.</au><au>Madej, Thomas</au><au>Panchenko, Anna R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2012-01-01</date><risdate>2012</risdate><volume>40</volume><issue>D1</issue><spage>D834</spage><epage>D840</epage><pages>D834-D840</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>22102591</pmid><doi>10.1093/nar/gkr997</doi><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0305-1048
ispartof Nucleic acids research, 2012-01, Vol.40 (D1), p.D834-D840
issn 0305-1048
1362-4962
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3245142
source OUP_牛津大学出版社OA刊; MEDLINE; Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry
subjects Binding Sites
Computer Graphics
Databases, Protein
Ions - chemistry
Molecular Sequence Annotation
Multiprotein Complexes - chemistry
Nucleic Acids - chemistry
Peptides - chemistry
Protein Interaction Mapping
Proteins - chemistry
Sequence Analysis, Protein
Systems Integration
User-Computer Interface
title IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T10%3A34%3A37IST&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=IBIS%20(Inferred%20Biomolecular%20Interaction%20Server)%20reports,%20predicts%20and%20integrates%20multiple%20types%20of%20conserved%20interactions%20for%20proteins&rft.jtitle=Nucleic%20acids%20research&rft.au=Shoemaker,%20Benjamin%20A.&rft.date=2012-01-01&rft.volume=40&rft.issue=D1&rft.spage=D834&rft.epage=D840&rft.pages=D834-D840&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gkr997&rft_dat=%3Cproquest_pubme%3E912642787%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=912642787&rft_id=info:pmid/22102591&rft_oup_id=10.1093/nar/gkr997&rfr_iscdi=true