The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation

Genome Biology
Shirley WuRuss B Altman

Abstract

Structural genomics efforts have led to increasing numbers of novel, uncharacterized protein structures with low sequence identity to known proteins, resulting in a growing need for structure-based function recognition tools. Our method, SeqFEATURE, robustly models protein functions described by sequence motifs using a structural representation. We built a library of models that shows good performance compared to other methods. In particular, SeqFEATURE demonstrates significant improvement over other methods when sequence and structural similarity are low.

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Citations

Nov 19, 2009·Drug Design, Development and Therapy·Olivia Doppelt-AzeroualAlexandre G de Brevern
Apr 25, 2012·Annual Review of Analytical Chemistry·Bryant GipsonJean-Claude Latombe
Jul 20, 2011·Proteins·Russell SpitzerAjay N Jain
Feb 18, 2010·Protein Science : a Publication of the Protein Society·Olivia Doppelt-AzeroualAlexandre G de Brevern
Feb 9, 2017·Bioscience Reports·Gunseli Bayram Akcapinar, Osman Ugur Sezerman

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Methods Mentioned

BETA
structure-based prediction

Software Mentioned

ProKnow
Perl
Superfamily
Pfam
InterPro
SSM
PROSITE
Smith
PSI
Gene3D

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