title: PRUNE and PROBE--two modular web services for protein-protein docking.
abstract: The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate >95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.
authors.affiliation: Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.
authors.forename: Pralay
authors.initials: P
authors.lastname: Mitra
authors.forename: Debnath
authors.initials: D
authors.lastname: Pal
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D046912:Multiprotein Complexes