Using linear algebra for protein structural comparison and classification.

Vista sencilla de ítem
dc.contributorJANAÍNA GOMIDE, UFMG; RAQUEL MELO-MINARDI, UFMG; MARCOS AUGUSTO DOS SANTOS, UFMG; GORAN NESHICH, CNPTIA; WAGNER MEIRA JUNIOR, UFMG; JÚLIO CÉSAR LOPES, UFMG; MARCELO SANTORO, UFMG.
dc.creatorGOMIDE, J.
dc.creatorMELO-MINARDI, R.
dc.creatorSANTOS, M. A. dos
dc.creatorNESHICH, G.
dc.creatorMEIRA JUNIOR, W.
dc.creatorLOPES, J. C.
dc.creatorSANTORO, M.
dc.date2011-04-10T11:11:11Z
dc.date2011-04-10T11:11:11Z
dc.date2010-04-15
dc.date2009
dc.date2016-09-29T11:11:11Z
dc.date.accessioned2026-07-07T04:14:38Z
dc.descriptionIn this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.
dc.identifierGenetics and Molecular Biology, v. 32, n. 3, p. 645-651, 2009.
dc.identifierhttp://www.alice.cnptia.embrapa.br/alice/handle/doc/664383
dc.identifierhttp://dx.doi.org/10.1590/S1415-47572009000300032
dc.identifier.urihttp://hdl.handle.net/123456789/455257
dc.languageeng
dc.rightsopenAccess
dc.subjectProtein classification
dc.subjectContact maps
dc.subjectLinear algebra
dc.subjectSingular value decomposition
dc.subjectLatent semantic indexing
dc.subjectBiologia molecular
dc.subjectMolecular biology
dc.titleUsing linear algebra for protein structural comparison and classification.
dc.typeArtigo de periódico

Archivos

Colecciones

Embrapa Agricultura Digital (CNPTIA)