A contact map matching approach to protein structure similarity analysis
We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-proces...
Gespeichert in:
| Veröffentlicht in: | Genetics and molecular research 2006-06, Vol.5 (2), p.284-308 |
|---|---|
| Hauptverfasser: | , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 308 |
|---|---|
| container_issue | 2 |
| container_start_page | 284 |
| container_title | Genetics and molecular research |
| container_volume | 5 |
| creator | de Melo, Raquel C Lopes, Carlos Eduardo R Fernandes, Jr, Fernando A da Silveira, Carlos Henrique Santoro, Marcelo M Carceroni, Rodrigo L Meira, Jr, Wagner Araújo, Arnaldo de A |
| description | We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure the dissimilarity between these contact maps; one was a content-based image retrieval method, and the other was based on image registration. In experiments with contact maps constructed from the protein data bank, our approach was able to identify, with greater than 80% precision, instances of monomers of apolipoproteins, globins, plastocyanins, retinol binding proteins and thioredoxins, among the monomers of Protein Data Bank Select. The image registration approach was only slightly more accurate than the content-based image retrieval approach. |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_proquest_miscellaneous_68605989</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>68605989</sourcerecordid><originalsourceid>FETCH-LOGICAL-p209t-154ea04743329358279333504ad47f5de707da05fdceb69160471799d7a4d0d63</originalsourceid><addsrcrecordid>eNo1j01LAzEYhIMgtlb_guTkbeHN5vtYilqh0Iuel7dJ1kb2yyR76L93wXoYZg4Pw8wNWTOlVSWVgRW5z_kboJbCwB1ZMWWY1WDXZL-lbhwKukJ7nBYVd47DF8VpSiO6My0jXVIJcaC5pNmVOQWaYx87TLFcKA7YXXLMD-S2xS6Hx6tvyOfry8duXx2Ob--77aGaarClYlIEBKEF57Xl0tTacs4lCPRCt9IHDdojyNa7cFKWqYVl2lqvUXjwim_I81_vsupnDrk0fcwudB0OYZxzo4wCaY1dwKcrOJ_64JspxR7Tpfn_zn8BnatUNA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>68605989</pqid></control><display><type>article</type><title>A contact map matching approach to protein structure similarity analysis</title><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><creator>de Melo, Raquel C ; Lopes, Carlos Eduardo R ; Fernandes, Jr, Fernando A ; da Silveira, Carlos Henrique ; Santoro, Marcelo M ; Carceroni, Rodrigo L ; Meira, Jr, Wagner ; Araújo, Arnaldo de A</creator><creatorcontrib>de Melo, Raquel C ; Lopes, Carlos Eduardo R ; Fernandes, Jr, Fernando A ; da Silveira, Carlos Henrique ; Santoro, Marcelo M ; Carceroni, Rodrigo L ; Meira, Jr, Wagner ; Araújo, Arnaldo de A</creatorcontrib><description>We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure the dissimilarity between these contact maps; one was a content-based image retrieval method, and the other was based on image registration. In experiments with contact maps constructed from the protein data bank, our approach was able to identify, with greater than 80% precision, instances of monomers of apolipoproteins, globins, plastocyanins, retinol binding proteins and thioredoxins, among the monomers of Protein Data Bank Select. The image registration approach was only slightly more accurate than the content-based image retrieval approach.</description><identifier>EISSN: 1676-5680</identifier><identifier>PMID: 16819709</identifier><language>eng</language><publisher>Brazil</publisher><subject>Algorithms ; Computer Simulation ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Proteins - chemistry ; Sequence Alignment - methods ; Sequence Analysis, Protein ; Structure-Activity Relationship</subject><ispartof>Genetics and molecular research, 2006-06, Vol.5 (2), p.284-308</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16819709$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>de Melo, Raquel C</creatorcontrib><creatorcontrib>Lopes, Carlos Eduardo R</creatorcontrib><creatorcontrib>Fernandes, Jr, Fernando A</creatorcontrib><creatorcontrib>da Silveira, Carlos Henrique</creatorcontrib><creatorcontrib>Santoro, Marcelo M</creatorcontrib><creatorcontrib>Carceroni, Rodrigo L</creatorcontrib><creatorcontrib>Meira, Jr, Wagner</creatorcontrib><creatorcontrib>Araújo, Arnaldo de A</creatorcontrib><title>A contact map matching approach to protein structure similarity analysis</title><title>Genetics and molecular research</title><addtitle>Genet Mol Res</addtitle><description>We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure the dissimilarity between these contact maps; one was a content-based image retrieval method, and the other was based on image registration. In experiments with contact maps constructed from the protein data bank, our approach was able to identify, with greater than 80% precision, instances of monomers of apolipoproteins, globins, plastocyanins, retinol binding proteins and thioredoxins, among the monomers of Protein Data Bank Select. The image registration approach was only slightly more accurate than the content-based image retrieval approach.</description><subject>Algorithms</subject><subject>Computer Simulation</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Protein Conformation</subject><subject>Proteins - chemistry</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, Protein</subject><subject>Structure-Activity Relationship</subject><issn>1676-5680</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo1j01LAzEYhIMgtlb_guTkbeHN5vtYilqh0Iuel7dJ1kb2yyR76L93wXoYZg4Pw8wNWTOlVSWVgRW5z_kboJbCwB1ZMWWY1WDXZL-lbhwKukJ7nBYVd47DF8VpSiO6My0jXVIJcaC5pNmVOQWaYx87TLFcKA7YXXLMD-S2xS6Hx6tvyOfry8duXx2Ob--77aGaarClYlIEBKEF57Xl0tTacs4lCPRCt9IHDdojyNa7cFKWqYVl2lqvUXjwim_I81_vsupnDrk0fcwudB0OYZxzo4wCaY1dwKcrOJ_64JspxR7Tpfn_zn8BnatUNA</recordid><startdate>20060630</startdate><enddate>20060630</enddate><creator>de Melo, Raquel C</creator><creator>Lopes, Carlos Eduardo R</creator><creator>Fernandes, Jr, Fernando A</creator><creator>da Silveira, Carlos Henrique</creator><creator>Santoro, Marcelo M</creator><creator>Carceroni, Rodrigo L</creator><creator>Meira, Jr, Wagner</creator><creator>Araújo, Arnaldo de A</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope></search><sort><creationdate>20060630</creationdate><title>A contact map matching approach to protein structure similarity analysis</title><author>de Melo, Raquel C ; Lopes, Carlos Eduardo R ; Fernandes, Jr, Fernando A ; da Silveira, Carlos Henrique ; Santoro, Marcelo M ; Carceroni, Rodrigo L ; Meira, Jr, Wagner ; Araújo, Arnaldo de A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p209t-154ea04743329358279333504ad47f5de707da05fdceb69160471799d7a4d0d63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Algorithms</topic><topic>Computer Simulation</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>Sequence Alignment - methods</topic><topic>Sequence Analysis, Protein</topic><topic>Structure-Activity Relationship</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>de Melo, Raquel C</creatorcontrib><creatorcontrib>Lopes, Carlos Eduardo R</creatorcontrib><creatorcontrib>Fernandes, Jr, Fernando A</creatorcontrib><creatorcontrib>da Silveira, Carlos Henrique</creatorcontrib><creatorcontrib>Santoro, Marcelo M</creatorcontrib><creatorcontrib>Carceroni, Rodrigo L</creatorcontrib><creatorcontrib>Meira, Jr, Wagner</creatorcontrib><creatorcontrib>Araújo, Arnaldo de A</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><jtitle>Genetics and molecular research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>de Melo, Raquel C</au><au>Lopes, Carlos Eduardo R</au><au>Fernandes, Jr, Fernando A</au><au>da Silveira, Carlos Henrique</au><au>Santoro, Marcelo M</au><au>Carceroni, Rodrigo L</au><au>Meira, Jr, Wagner</au><au>Araújo, Arnaldo de A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A contact map matching approach to protein structure similarity analysis</atitle><jtitle>Genetics and molecular research</jtitle><addtitle>Genet Mol Res</addtitle><date>2006-06-30</date><risdate>2006</risdate><volume>5</volume><issue>2</issue><spage>284</spage><epage>308</epage><pages>284-308</pages><eissn>1676-5680</eissn><abstract>We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure the dissimilarity between these contact maps; one was a content-based image retrieval method, and the other was based on image registration. In experiments with contact maps constructed from the protein data bank, our approach was able to identify, with greater than 80% precision, instances of monomers of apolipoproteins, globins, plastocyanins, retinol binding proteins and thioredoxins, among the monomers of Protein Data Bank Select. The image registration approach was only slightly more accurate than the content-based image retrieval approach.</abstract><cop>Brazil</cop><pmid>16819709</pmid><tpages>25</tpages></addata></record> |
| fulltext | fulltext |
| identifier | EISSN: 1676-5680 |
| ispartof | Genetics and molecular research, 2006-06, Vol.5 (2), p.284-308 |
| issn | 1676-5680 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_68605989 |
| source | MEDLINE; EZB-FREE-00999 freely available EZB journals |
| subjects | Algorithms Computer Simulation Models, Chemical Models, Molecular Protein Conformation Proteins - chemistry Sequence Alignment - methods Sequence Analysis, Protein Structure-Activity Relationship |
| title | A contact map matching approach to protein structure similarity analysis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-13T23%3A57%3A32IST&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=A%20contact%20map%20matching%20approach%20to%20protein%20structure%20similarity%20analysis&rft.jtitle=Genetics%20and%20molecular%20research&rft.au=de%20Melo,%20Raquel%20C&rft.date=2006-06-30&rft.volume=5&rft.issue=2&rft.spage=284&rft.epage=308&rft.pages=284-308&rft.eissn=1676-5680&rft_id=info:doi/&rft_dat=%3Cproquest_pubme%3E68605989%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=68605989&rft_id=info:pmid/16819709&rfr_iscdi=true |