Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation |
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Authors: | Albert Solernou Juan Fernandez-Recio |
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Institution: | (1) Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain |
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Abstract: | Background Protein-protein interactions are fundamental for the majority of cellular processes and their study is of enormous biotechnological
and therapeutic interest. In recent years, a variety of computational approaches to the protein-protein docking problem have
been reported, with encouraging results. Most of the currently available protein-protein docking algorithms are composed of
two clearly defined parts: the sampling of the rotational and translational space of the interacting molecules, and the scoring
and clustering of the resulting orientations. Although this kind of strategy has shown some of the most successful results
in the CAPRI blind test , more efforts need to be applied. Thus, the sampling protocol should generate a pool of conformations that include a sufficient
number of near-native ones, while the scoring function should discriminate between near-native and non-near-native proposed
conformations. On the other hand, protocols to efficiently include full flexibility on the protein structures are increasingly
needed. |
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Keywords: | |
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