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
Affiliations:
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
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2013

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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.