Computational Tools for Exploration of the Energy Landscape in Protein-Protein Association
- Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, E-08034, Barcelona (Spain)
We show here our work in structural prediction of protein-protein interactions. Our computational docking methodology has two major components: the sampling of mutual orientations of the interacting molecules, and the scoring and clustering of these orientations for the identification of near-native docking poses. Our procedure can generate a uniformly distributed set of rigid-body docking poses, which can be easily extended to explore the flexibility of the side-chains. The method is able to find near-native orientations in line with other state-of-the-art docking programs, and it has been successfully applied together with our pyDock scoring scheme in the most recent rounds of the CAPRI worl-wide experiment (http://capri.ebi.ac.uk). We have also devised a new measure to compare rigid-body docking poses based on angular distance (instead of RMSD), which describes the relative orientations of the two molecules in the different docking poses, as evaluated in a large benchmark of known protein-protein cases. The low computational cost of this measure (as compared with the RMSD calculation) makes it ideal for clustering docking poses in a more effective way. The new docking angular index of similarity (DASI) can also be used to evaluate the validity of the docking predictions, when comparing with the X-ray structures.
- OSTI ID:
- 21251771
- Journal Information:
- AIP Conference Proceedings, Vol. 1071, Issue 1; Conference: BIFI2008: International conference on large scale simulations of complex systems, condensed matter and fusion plasma, Zaragoza (Spain), 6-8 Feb 2008; Other Information: DOI: 10.1063/1.3033364; (c) 2008 American Institute of Physics; Country of input: International Atomic Energy Agency (IAEA); ISSN 0094-243X
- Country of Publication:
- United States
- Language:
- English
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