SitesIdentify: a protein functional site prediction tool
<p>Abstract</p> <p>Background</p> <p>The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Id...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-11-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/10/379 |
| _version_ | 1818142879003967488 |
|---|---|
| author | Doig Andrew J Greaves Richard Bougouffa Salim Chan Pedro Bray Tracey Warwicker Jim |
| author_facet | Doig Andrew J Greaves Richard Bougouffa Salim Chan Pedro Bray Tracey Warwicker Jim |
| author_sort | Doig Andrew J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application.</p> <p>Results</p> <p>Here we present a functional site prediction tool (SitesIdentify), based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites.</p> <p>Conclusion</p> <p>SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at <url>http://www.manchester.ac.uk/bioinformatics/sitesidentify/</url></p> |
| first_indexed | 2024-12-11T11:22:47Z |
| format | Article |
| id | doaj.art-156ec3fdf080438f89c2b1a46ac0b7a9 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T11:22:47Z |
| publishDate | 2009-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-156ec3fdf080438f89c2b1a46ac0b7a92022-12-22T01:09:05ZengBMCBMC Bioinformatics1471-21052009-11-0110137910.1186/1471-2105-10-379SitesIdentify: a protein functional site prediction toolDoig Andrew JGreaves RichardBougouffa SalimChan PedroBray TraceyWarwicker Jim<p>Abstract</p> <p>Background</p> <p>The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application.</p> <p>Results</p> <p>Here we present a functional site prediction tool (SitesIdentify), based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites.</p> <p>Conclusion</p> <p>SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at <url>http://www.manchester.ac.uk/bioinformatics/sitesidentify/</url></p>http://www.biomedcentral.com/1471-2105/10/379 |
| spellingShingle | Doig Andrew J Greaves Richard Bougouffa Salim Chan Pedro Bray Tracey Warwicker Jim SitesIdentify: a protein functional site prediction tool BMC Bioinformatics |
| title | SitesIdentify: a protein functional site prediction tool |
| title_full | SitesIdentify: a protein functional site prediction tool |
| title_fullStr | SitesIdentify: a protein functional site prediction tool |
| title_full_unstemmed | SitesIdentify: a protein functional site prediction tool |
| title_short | SitesIdentify: a protein functional site prediction tool |
| title_sort | sitesidentify a protein functional site prediction tool |
| url | http://www.biomedcentral.com/1471-2105/10/379 |
| work_keys_str_mv | AT doigandrewj sitesidentifyaproteinfunctionalsitepredictiontool AT greavesrichard sitesidentifyaproteinfunctionalsitepredictiontool AT bougouffasalim sitesidentifyaproteinfunctionalsitepredictiontool AT chanpedro sitesidentifyaproteinfunctionalsitepredictiontool AT braytracey sitesidentifyaproteinfunctionalsitepredictiontool AT warwickerjim sitesidentifyaproteinfunctionalsitepredictiontool |