A discrete search algorithm for finding the structure of protein backbones and side chains
by Silas Sallaume; Simone de Lima Martins; Luiz Satoru Ochi; Warley Gramacho Da Silva; Carlile Lavor; Leo Liberti
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 9, No. 3, 2013

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.

Online publication date: Sat, 06-Sep-2014

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