Journal article

A knowledge-based scoring function based on residue triplets for protein structure prediction

SC Ngan, MT Inouye, R Samudrala

PROTEIN ENGINEERING DESIGN & SELECTION | OXFORD UNIV PRESS | Published : 2006

Abstract

One of the general paradigms for ab initio protein structure prediction involves sampling the conformational space such that a large set of decoy (candidate) structures are generated and then selecting native-like conformations from those decoys using various scoring functions. In this study, based on a physical/geometric approach first suggested by Banavar and colleagues, we formulate a knowledge-based scoring function, which uses the radii of curvature formed among triplets of residues in a protein conformation. By analyzing its performance on various decoy sets, we determine a good set of parameters--the distance cutoff and the number of distance bins--to use for configuring such a functi..

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University of Melbourne Researchers