Title |
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
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Published in |
BMC Bioinformatics, March 2012
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DOI | 10.1186/1471-2105-13-39 |
Pubmed ID | |
Authors |
Paul Ashford, David S Moss, Alexander Alex, Siew K Yeap, Alice Povia, Irene Nobeli, Mark A Williams |
Abstract |
Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins' dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pocket's boundaries. For a set of conformationally distinct structures the challenge is how to make reasonable comparisons between them given that a perfect structural alignment is not possible. |
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Demographic breakdown
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Mendeley readers
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Researcher | 17 | 27% |
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Student > Bachelor | 2 | 3% |
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Engineering | 4 | 6% |
Other | 4 | 6% |
Unknown | 5 | 8% |