Faculty Publications

Title

SPINFAST: Using structure alignment profiles to enhance the accuracy and assess the reliability of protein side-chain modeling

Document Type

Article

Keywords

Dihedral angles, Homology modeling, Rotamer library, Side-chains, Structure prediction

Journal/Book/Conference Title

Proteins: Structure, Function and Genetics

Volume

65

Issue

4

First Page

953

Last Page

958

Abstract

We present a novel, knowledge-based method for the side-chain addition step in protein structure modeling. The foundation of the method is a conditional probability equation, which specifies the probability that a side-chain will occupy a specific rotamer state, given a set of evidence about the rotamer states adopted by the side-chains at aligned positions in structurally homologous crystal structures. We demonstrate that our method increases the accuracy of homology model side-chain addition when compared with the widely employed practice of preserving the side-chain conformation from the homology template to the target at conserved residue positions. Furthermore, we demonstrate that our method accurately estimates the probability that the correct rotamer state has been selected. This interesting result implies that our method can be used to understand the reliability of each and every side-chain in a protein homology model. © 2005 Wiley-Liss, Inc.

Original Publication Date

12-1-2006

DOI of published version

10.1002/prot.21154

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