FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families
Identifieur interne : 002D68 ( Main/Exploration ); précédent : 002D67; suivant : 002D69FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families
Auteurs : Timothy Luciani [États-Unis] ; John Wenskovitch [États-Unis] ; Koonwah Chen [États-Unis] ; David Koes [États-Unis] ; Timothy Travers [États-Unis] ; G Elisabeta Marai [États-Unis]Source :
- BMC Proceedings [ 1753-6561 ] ; 2014.
Abstract
Knowledge of the 3D structure and functionality of proteins can lead to insight into the associated cellular processes, speed up the creation of pharmaceutical products, and develop drugs that are more effective in combating disease.
We present the design and implementation of a visual mining and analysis tool to help identify protein mutations across a family of structural models and to help discover the effect of these mutations on protein function. We integrate 3D structure and sequence information in a common visual interface; multiple linked views and a computational backbone allow comparison at the molecular and atomic levels, while a novel trend-image visual abstraction allows for the sorting and mining of large collections of sequences and of their residues.
We evaluate our approach on the triosephosphate isomerase (TIM) family structural models and sequence data and show that our tool provides an effective, scalable way to navigate a family of proteins, as well as a means to inspect the structure and sequence of individual proteins.
The TIM application shows that our tool can assist in the navigation of families of proteins, as well as in the exploration of individual protein structures. In conjunction with domain expert knowledge, this interactive tool can help provide biophysical insight into why specific mutations affect function and potentially suggest additional modifications to the protein that could be used to rescue functionality.
Url:
DOI: 10.1186/1753-6561-8-S2-S3
PubMed: 25237390
PubMed Central: 4155608
Affiliations:
- États-Unis
- Illinois, Pennsylvanie, Rhode Island
- Chicago, Pittsburgh, Providence (Rhode Island)
- Université Brown, Université de Pittsburgh, Université de l'Illinois à Chicago
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Le document en format XML
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families</title><author><name sortKey="Luciani, Timothy" sort="Luciani, Timothy" uniqKey="Luciani T" first="Timothy" last="Luciani">Timothy Luciani</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Computer Science, Brown University, Box 1910, 02912 Providence, RI, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Brown University, Box 1910, 02912 Providence, RI</wicri:regionArea><placeName><region type="state">Rhode Island</region><settlement type="city">Providence (Rhode Island)</settlement></placeName><orgName type="university">Université Brown</orgName></affiliation></author><author><name sortKey="Wenskovitch, John" sort="Wenskovitch, John" uniqKey="Wenskovitch J" first="John" last="Wenskovitch">John Wenskovitch</name><affiliation wicri:level="4"><nlm:aff id="I2">Department of Computer Science, University of Pittsburgh, 210 South Bouquet, 15260 Pittsburgh, PA, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, University of Pittsburgh, 210 South Bouquet, 15260 Pittsburgh, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Chen, Koonwah" sort="Chen, Koonwah" uniqKey="Chen K" first="Koonwah" last="Chen">Koonwah Chen</name><affiliation wicri:level="4"><nlm:aff id="I3">School of Information Science, University of Pittsburgh, 135 North Bellefield Avenue, 15260 Pittsburgh, PA, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Information Science, University of Pittsburgh, 135 North Bellefield Avenue, 15260 Pittsburgh, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Koes, David" sort="Koes, David" uniqKey="Koes D" first="David" last="Koes">David Koes</name><affiliation wicri:level="4"><nlm:aff id="I4">Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, 15260 Pittsburgh, PA, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, 15260 Pittsburgh, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Travers, Timothy" sort="Travers, Timothy" uniqKey="Travers T" first="Timothy" last="Travers">Timothy Travers</name><affiliation wicri:level="4"><nlm:aff id="I4">Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, 15260 Pittsburgh, PA, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, 15260 Pittsburgh, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Marai, G Elisabeta" sort="Marai, G Elisabeta" uniqKey="Marai G" first="G Elisabeta" last="Marai">G Elisabeta Marai</name><affiliation wicri:level="4"><nlm:aff id="I5">Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St., 60607 Chicago, IL, US</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St., 60607 Chicago, IL</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">Chicago</settlement></placeName><orgName type="university">Université de l'Illinois à Chicago</orgName></affiliation></author></analytic><series><title level="j">BMC Proceedings</title><idno type="eISSN">1753-6561</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Knowledge of the 3D structure and functionality of proteins can lead to insight into the associated cellular processes, speed up the creation of pharmaceutical products, and develop drugs that are more effective in combating disease.</p></sec><sec><title>Methods</title><p>We present the design and implementation of a visual mining and analysis tool to help identify protein mutations across a family of structural models and to help discover the effect of these mutations on protein function. We integrate 3D structure and sequence information in a common visual interface; multiple linked views and a computational backbone allow comparison at the molecular and atomic levels, while a novel trend-image visual abstraction allows for the sorting and mining of large collections of sequences and of their residues.</p></sec><sec><title>Results</title><p>We evaluate our approach on the triosephosphate isomerase (TIM) family structural models and sequence data and show that our tool provides an effective, scalable way to navigate a family of proteins, as well as a means to inspect the structure and sequence of individual proteins.</p></sec><sec><title>Conclusions</title><p>The TIM application shows that our tool can assist in the navigation of families of proteins, as well as in the exploration of individual protein structures. In conjunction with domain expert knowledge, this interactive tool can help provide biophysical insight into why specific mutations affect function and potentially suggest additional modifications to the protein that could be used to rescue functionality.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhong, W" uniqKey="Zhong W">W Zhong</name></author><author><name sortKey="Altum, G" uniqKey="Altum G">G Altum</name></author><author><name sortKey="Harrison, R" uniqKey="Harrison R">R Harrison</name></author><author><name sortKey="Tai, Pc" uniqKey="Tai P">PC Tai</name></author><author><name sortKey="Pan, Y" uniqKey="Pan Y">Y Pan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, N" uniqKey="Chen N">N Chen</name></author><author><name sortKey="Harris, Tw" uniqKey="Harris T">TW Harris</name></author><author><name sortKey="Antoshechkin, I" uniqKey="Antoshechkin I">I 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sortKey="Travers, Timothy" sort="Travers, Timothy" uniqKey="Travers T" first="Timothy" last="Travers">Timothy Travers</name><name sortKey="Wenskovitch, John" sort="Wenskovitch, John" uniqKey="Wenskovitch J" first="John" last="Wenskovitch">John Wenskovitch</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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