Title: A discrete search algorithm for finding the structure of protein backbones and side chains

Authors: Silas Sallaume; Simone de Lima Martins; Luiz Satoru Ochi; Warley Gramacho Da Silva; Carlile Lavor; Leo Liberti

Addresses: Departamento de Ciência da Computação, Faculdades Thathi, Araçatuba – SP, Brazil ' Departamento de Ciência da Computação, Universidade Federal Fluminense, Niterói – RJ, Brazil ' Departamento de Ciência da Computação, Universidade Federal Fluminense, Niterói – RJ, Brazil ' Campus Universitário de Palmas, Universidade Federal do Tocantins, Palmas – TO, Brazil ' Departamento de Matemática Aplicada, Universidade Estadual de Campinas, Campinas – SP, Brazil ' LIX, École Polytechnique, F-91128 Palaiseau, France

Abstract: Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

Keywords: bioinformatics; branch and prune algorithms; discretisable molecular distance geometry; 3D protein structure; computational physical chemistry; discrete search; protein backbones; protein side chains.

DOI: 10.1504/IJBRA.2013.053606

International Journal of Bioinformatics Research and Applications, 2013 Vol.9 No.3, pp.261 - 270

Received: 24 Mar 2011
Accepted: 15 Aug 2011
Published online: 06 Sep 2014 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article