NDLI: Surface-histogram: A new shape descriptor for protein-protein docking

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Surface-histogram: A new shape descriptor for protein-protein docking

Content Provider	Scilit
Author	Gu, Shengyin Koehl, Patrice Hass, Joel Amenta, Nina
Copyright Year	2011
Description	Journal: Proteins: Structure, Function, and Bioinformatics 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.
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240741/pdf
Ending Page	238
Page Count	18
Starting Page	221
e-ISSN	10970134
DOI	10.1002/prot.23192
Journal	Proteins: Structure, Function, and Bioinformatics
Issue Number	1
Volume Number	80
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2011-11-09
Access Restriction	Open
Subject Keyword	Journal: Proteins: Structure, Function, and Bioinformatics Protein-protein Docking Surface-histogram
Content Type	Text
Resource Type	Article

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