Andrea Cassioli1, Benjamin Bardiaux2,3, Guillaume Bouvier4,5, Antonio Mucherino6, Rafael Alves7, Leo Liberti8,9, Michael Nilges10,11, Carlile Lavor12, Thérèse E Malliavin13,14. 1. LIX, Ecole Polytechnique, Palaiseau, 91128, France. cassioliandre@gmail.com. 2. Institut Pasteur, Structural Bioinformatics Unit, 25, rue du Dr Roux, Paris, 75015, France. benjamin.bardiaux@pasteur.fr. 3. CNRS UMR3528, 25, rue du Dr Roux, Paris, 75015, France. benjamin.bardiaux@pasteur.fr. 4. Institut Pasteur, Structural Bioinformatics Unit, 25, rue du Dr Roux, Paris, 75015, France. guillaume.bouvier@pasteur.fr. 5. CNRS UMR3528, 25, rue du Dr Roux, Paris, 75015, France. guillaume.bouvier@pasteur.fr. 6. Université de Rennes-I, Rennes, France. antonio.mucherino@irisa.fr. 7. LIX, Ecole Polytechnique, Palaiseau, 91128, France. rafaelsoalves@uol.com.br. 8. LIX, Ecole Polytechnique, Palaiseau, 91128, France. liberti@lix.polytechnique.fr. 9. IBM TJ Watson Research Center, NY Yorktown Heights, 10598, USA. liberti@lix.polytechnique.fr. 10. Institut Pasteur, Structural Bioinformatics Unit, 25, rue du Dr Roux, Paris, 75015, France. michael.nilges@pasteur.fr. 11. CNRS UMR3528, 25, rue du Dr Roux, Paris, 75015, France. michael.nilges@pasteur.fr. 12. University of Campinas (IMECC-UNICAMP), Campinas-SP, 13083-859, Brasil. clavor@ime.unicamp.br. 13. Institut Pasteur, Structural Bioinformatics Unit, 25, rue du Dr Roux, Paris, 75015, France. therese.malliavin@pasteur.fr. 14. CNRS UMR3528, 25, rue du Dr Roux, Paris, 75015, France. therese.malliavin@pasteur.fr.
Abstract
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 (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. CONCLUSIONS: 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.
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 (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. CONCLUSIONS: 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.
Authors: Xi Huang; Manuel D Britto; Jamie L Kear-Scott; Christopher D Boone; James R Rocca; Carlos Simmerling; Robert Mckenna; Michael Bieri; Paul R Gooley; Ben M Dunn; Gail E Fanucci Journal: J Biol Chem Date: 2014-04-17 Impact factor: 5.157