Jonathan A Barker1, Janet M Thornton. 1. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. jbarker@ebi.ac.uk
Abstract
MOTIVATION: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly. RESULTS: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.
MOTIVATION: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly. RESULTS: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.
Authors: James D Watson; Annabel E Todd; James Bray; Roman A Laskowski; Aled Edwards; Andrzej Joachimiak; Christine A Orengo; Janet M Thornton Journal: IUBMB Life Date: 2003 Apr-May Impact factor: 3.885
Authors: David M Kristensen; Brian Y Chen; Viacheslav Y Fofanov; R Matthew Ward; Andreas Martin Lisewski; Marek Kimmel; Lydia E Kavraki; Olivier Lichtarge Journal: Protein Sci Date: 2006-05-02 Impact factor: 6.725
Authors: Deepak Bandyopadhyay; Jun Huan; Jan Prins; Jack Snoeyink; Wei Wang; Alexander Tropsha Journal: J Comput Aided Mol Des Date: 2009-06-20 Impact factor: 3.686