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SitCon: binding site residue conservation visualization and protein sequence-to-function tool

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dc.contributor.authorKairys, Visvaldas
dc.contributor.authorFernandes, Miguel X.
dc.date.accessioned2023-02-06T17:08:29Z
dc.date.available2023-02-06T17:08:29Z
dc.date.issued2007
dc.description.abstractWe introduce SitCon (SITe CONservation), a program designed to explore conservation of functionally important sites in a series of hypothetically homologous candidate protein structures, given amino acid sequence as an input. This can especially be useful when looking for an unknown function of a protein. SitCon exploits the fact that binding sites of proteins are preserved better than the overall residue sequence conservation. To test the capability of unknown function prediction, we randomly chose known function proteins from Caenorhabditis elegans genome. To imitate a behavior of an unknown function target, only the low homology proteins with 0.01 E-score 100 were analyzed as templates. Out of 29 enzyme targets, SitCon was able to provide various hints about their function in at least 69% of the cases. For the eight nonenzyme targets, the predictions matched in only 25% of the cases. SitCon was also tested for a capability to predict presence or absence of metal-containing heterogroups in the target enzymes with 80% success rate. Because this algorithm is not based on specific protein signatures, it may allow detection of overlooked relationships between proteins. SitCon is also very effective as a tool allowing visual comparison of binding site residue conservation between the target and homologous templates side-by-side.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationKairys, V., & Fernandes, M. X. (2007). SitCon: Binding site residue conservation visualization and protein sequence‐to‐function tool. International Journal of Quantum Chemistry, 107(11), 2100-2110.pt_PT
dc.identifier.doi10.1002/qua.21396pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.13/5004
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.relationINTEGRATION OF GENOMIC AND STRUCTURAL INFORMATION TO CHOOSE NEW THERAPEUTICAL TARGETS AND DEVELOP NEW DRUGS AGAINST MALARIA
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/pt_PT
dc.subjectGenomept_PT
dc.subjectSequence-to-functionpt_PT
dc.subjectProtein function predictionpt_PT
dc.subjectBinding sitept_PT
dc.subjectAmino acid residue conservationpt_PT
dc.subject.pt_PT
dc.subjectFaculdade de Ciências Exatas e da Engenhariapt_PT
dc.titleSitCon: binding site residue conservation visualization and protein sequence-to-function toolpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleINTEGRATION OF GENOMIC AND STRUCTURAL INFORMATION TO CHOOSE NEW THERAPEUTICAL TARGETS AND DEVELOP NEW DRUGS AGAINST MALARIA
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F20716%2F2004/PT
oaire.citation.endPage2110pt_PT
oaire.citation.issue11pt_PT
oaire.citation.startPage2100pt_PT
oaire.citation.titleInternational Journal of Quantum Chemistrypt_PT
oaire.citation.volume107pt_PT
person.familyNameKairys
person.familyNameFernandes
person.givenNameVisvaldas
person.givenNameMiguel Xavier
person.identifierK-9893-2013
person.identifier.ciencia-idA716-F916-AFB2
person.identifier.ciencia-idED1D-3C7A-467C
person.identifier.orcid0000-0002-5427-0175
person.identifier.orcid0000-0002-1840-616X
person.identifier.ridA-4373-2013
person.identifier.scopus-author-id6602925161
person.identifier.scopus-author-id35466972500
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication43821a45-10cf-4dbd-bc5a-fa88d146fc36
relation.isAuthorOfPublication8dab9a0d-f44a-4d2d-b9b1-7b3145162ca3
relation.isAuthorOfPublication.latestForDiscovery43821a45-10cf-4dbd-bc5a-fa88d146fc36
relation.isProjectOfPublication093fc438-931a-4a7f-9470-a4ec3af929f3
relation.isProjectOfPublication.latestForDiscovery093fc438-931a-4a7f-9470-a4ec3af929f3

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