Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

Proteins
Jeffrey SkolnickYang Zhang

Abstract

This article describes the PROSPECTOR_3 threading algorithm, which combines various scoring functions designed to match structurally related target/template pairs. Each variant described was found to have a Z-score above which most identified templates have good structural (threading) alignments, Z(struct) (Z(good)). 'Easy' targets with accurate threading alignments are identified as single templates with Z > Z(good) or two templates, each with Z > Z(struct), having a good consensus structure in mutually aligned regions. 'Medium' targets have a pair of templates lacking a consensus structure, or a single template for which Z(struct) < Z < Z(good). PROSPECTOR_3 was applied to a comprehensive Protein Data Bank (PDB) benchmark composed of 1491 single domain proteins, 41-200 residues long and no more than 30% identical to any threading template. Of the proteins, 878 were found to be easy targets, with 761 having a root mean square deviation (RMSD) from native of less than 6.5 A. The average contact prediction accuracy was 46%, and on average 17.6 residue continuous fragments were predicted with RMSD values of 2.0 A. There were 606 medium targets identified, 87% (31%) of which had good structural (threading) alignments. On average, ...Continue Reading

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Citations

Sep 22, 2010·Journal of Chemical Information and Modeling·Michal Brylinski, Jeffrey Skolnick
Dec 18, 2012·Journal of Chemical Information and Modeling·Hongyi Zhou, Jeffrey Skolnick
Oct 21, 2010·Molecular Pharmaceutics·Michal Brylinski, Jeffrey Skolnick
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Aug 21, 2007·Proteins·Hongyi ZhouJeffrey Skolnick

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