An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

Background 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...

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Published in:BMC bioinformatics Vol. 16; no. 1; p. 23
Main Authors: Cassioli, Andrea, Bardiaux, Benjamin, Bouvier, Guillaume, Mucherino, Antonio, Alves, Rafael, Liberti, Leo, Nilges, Michael, Lavor, Carlile, Malliavin, Thérèse E
Format: Journal Article
Language:English
Published: London BioMed Central 28.01.2015
BioMed Central Ltd
Subjects:
Algorithms
Analysis
Biochemistry, Molecular Biology
Bioinformatics
Biomedical and Life Sciences
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer Simulation
Humans
Life Sciences
Methodology
Methodology Article
Microarrays
Models, Molecular
Molecular biology
Peptide Fragments - chemistry
Protein Conformation
Proteins - chemistry
Molecular conformation
Distance geometry
Nuclear magnetic resonance
Branch-and-prune algorithm
Protein structure
branch-and-prune algorithm
Nuclear Magnetic Resonance 1 2
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:Background 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. Results In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm ( i BP) 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. Conclusions We described the new algorithm i BP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm i BP has been applied on three α -helical peptides.
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content type line 23
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-015-0451-1