Celebratio Mathematica — Hass — Complete Bibliography

Complete Bibliography

Works connected to Shengyin Gu

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P. Francis-Lyon, S. Gu, J. Hass, N. Amenta, and P. Koehl: “Sampling the conformation of protein surface residues for flexible protein docking,” BMC Bioinform. 11 (2010), pp. 575–588. article

Nina Amenta	Related
Patricia Francis-Lyon	Related
Shengyin Gu	Related
Patrice Koehl	Related

S. Gu, P. Koehl, J. Hass, and N. Amenta: “Surface-histogram: A new shape descriptor for protein-protein docking,” Proteins Struct. Funct. Bioinf. 80 : 1 (January 2012), pp. 221–238. article

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.

Nina Amenta	Related
Shengyin Gu	Related
Patrice Koehl	Related