Title: Mining the Protein Data Bank with CReF to predict approximate 3-D structures of polypeptides

Authors: Marcio Dorn, Osmar Norberto De Souza

Addresses: Laboratorio de Bioinformatica, Modelagem e Simulacao de Biossistemas – LABIO, Programa de Pos-Graduacao em Ciencia da Computacao, Faculdade de Informatica, Pontificia Universidade Catolica do Rio Grande do Sul, Avenida Ipiranga, 6681, Predio 32 – Sala 602, CEP 90619-900, Porto Alegre, RS, Brazil. ' Laboratorio de Bioinformatica, Modelagem e Simulacao de Biossistemas – LABIO, Programa de Pos-Graduacao em Ciencia da Computacao, Faculdade de Informatica, Pontificia Universidade Catolica do Rio Grande do Sul, Avenida Ipiranga, 6681, Predio 32 – Sala 602, CEP 90619-900, Porto Alegre, RS, Brazil

Abstract: In this paper we describe CReF, a Central Residue Fragmentbased method to predict approximate 3-D structures of polypeptides by mining the Protein Data Bank (PDB). The approximate predicted structures are good enough to be used as starting conformations in refinement procedures employing state-of-the-art molecular mechanics methods such as molecular dynamics simulations. CReF is very fast and we illustrate its efficacy in three case studies of polypeptides whose sizes vary from 34 to 70 amino acids. As indicated by the RMSD values, our initial results show that the predicted structures adopt the expected fold, similar to the experimental ones.

Keywords: CReF; 3-D protein structure prediction; ab initio; de novo; knowledge-based methods; data mining; central residue fragment-based method; PDB; protein data bank; polypeptides; molecular dynamics.

DOI: 10.1504/IJDMB.2010.033521

International Journal of Data Mining and Bioinformatics, 2010 Vol.4 No.3, pp.281 - 299

Published online: 02 Jun 2010 *

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