Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/236011
Type: Artigo
Title: An algorithm to enumerate all possible protein conformations verifying a set of distance constraints
Author: Cassioli, Andrea
Bardiaux, Benjamin
Bouvier, Guillaume
Mucherino, Antonio
Alves, Rafael
Liberti, Leo
Nilges, Michael
Lavor, Carlile
Malliavin, Thérèse E
Abstract: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.
The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.
Subject: Proteínas - Conformação
Biologia computacional
Árvores (Teoria dos grafos)
Geometria de distâncias
Simulated annealing (Matemática)
Análise conformacional
Algoritmos branch-and-prune
Country: Reino Unido
Editor: Springer Nature
Citation: Bmc Bioinformatics. v. 16, p. 23, 2015.
Rights: aberto
Identifier DOI: 10.1186/s12859-015-0451-1
Address: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0451-1
Date Issue: 2015
Appears in Collections:IMECC - Artigos e Outros Documentos

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