Protein-Protein Docking

Informatics-driven Protein-protein Docking

Highlight of work led by I. Hashmig and A. Shehu* at ACM BCB-W Comput Struct Biol Workshop 2013, Proteome Sci J 2013, IEEE Intl Conf on Bioinf and Biomed (BIBM) 2012, J Bioinf and Comp Biol 2012, and IEEE BIBM-W Comput Struct Biol Workshop (CSBW) 2011.

We also design probabilistic search algorithms for the protein-protein docking problem. The goal is to predict functionally-relevant structures of assemblies formed by two or more protein units. This is an important problem, as molecules come together in higher-order structures to participate in chemical processes in the cell. Our approach is to separate the problem into two stages. The objective of the first stage is to map the configuration space with powerful probabilistic search algorithms. The key idea is to employ information on putative interaction interfaces in order to expedite the search and sample promising configurations in a rapid manner. The objective of the second stage is to integrate more sophisticated energy functions for refinement of selected promising structures. Details on this line of work can be found under the related pages and publications on our website.

On this Project:

  • Irina Hashmi

    Daniel Veltri

    Bahar Akbal-Delibas

    Nurit Haspel (Computer Science, UMass Boston)

    Nadine Kabbani(Neuroscience, GMU)

    Amarda Shehu

This material is based upon work supported by the National Science Foundation under IIS CAREER Award No. 1144106 to AS and Virginia Youth Tobacco Program (VYTP) Award to NK. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or VYTP.