title: Surface-histogram: a new shape descriptor for protein-protein docking.
abstract: Determining the structure of protein-protein complexes remains a difficult and lengthy process, either by NMR or by X-ray crystallography. Several computational methods based on docking have been developed to support and even serve as possible alternatives to these experimental methods. In this article, we introduce a new protein-protein docking algorithm, shDock, based on shape complementarity. We characterize the local geometry on each protein surface with a new shape descriptor, the surface-histogram. We measure the complementarity between two surface-histograms, one on each protein, using a modified Manhattan distance. When a match is found between two local protein surfaces, a model is generated for the protein complex, which is then scored by checking for collision between the two proteins. We have tested our algorithm on Version 3 of the ZDOCK protein-protein docking benchmark. We found that for 110 out of the 124 test cases of bound docking in the benchmark, our algorithm was able to generate a model in the top 3600 candidates for the protein complex within an root-mean-square deviation of 2.5 Å from its native structure. For unbound docking predictions, we found a model within 2.5 Å in the top 3600 models in 54 out of 124 test cases. A comparison with other shape-based docking algorithms demonstrates that our approach gives significantly improved performance for both bound and unbound docking test cases.
authors.affiliation: Department of Computer Science, University of California, Davis, California 95616, USA. sgu@ucdavis.edu
authors.forename: Shengyin
authors.initials: S
authors.lastname: Gu
authors.forename: Patrice
authors.initials: P
authors.lastname: Koehl
authors.forename: Joel
authors.initials: J
authors.lastname: Hass
authors.forename: Nina
authors.initials: N
authors.lastname: Amenta
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D044962:Data Compression; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D012984:Software; D013499:Surface Properties
chemical_list: D046912:Multiprotein Complexes
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