Identification of similar regions of protein structures using integrated sequence and structure analysis tools

BMC Structural Biology
Brandon PetersSean Mooney

Abstract

Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets AST...Continue Reading

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Citations

Nov 15, 2011·The Journal of Biological Chemistry·Michelle F S PintoOctávio L Franco
Jun 30, 2007·BMC Bioinformatics·Sungroh YoonRuss B Altman
Sep 5, 2015·Journal of Biomolecular Structure & Dynamics·Y Nanda KumarP Jambulingam
Sep 12, 2020·Microbial Pathogenesis·Sudipta Paul BhattacharyaAparna Sen
Oct 18, 2014·Chemical Research in Toxicology·Dharmendra S DheemanBarry P Rosen

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Methods Mentioned

BETA
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Software Mentioned

Delano Scientific PyMOL
BLEST
PSI
JMol
FEATURE
ProFunc
UCSF
BLAST PSSM
Structure Based Local Environment Search Tool ( S - BLEST )
CATH

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