Interface-targeted Assembly

This work has currently appeared in various publications. A preliminary study that shows the efficacy of combining evolutionary conservation and geometric analysis of molecular surfaces for determining putative interaction interfaces and tests these interfaces in the context of rigid protein-protein docking has appeared in: 1) Irina Hashmi, Bahar Aklbal-Delibas, Nurit Haspel, and Amarda Shehu. "Guiding Protein Docking with Geometric and Evolutionary Information." J Bioinf and Comp Biol 2012, 10(3): 1242002; and 2) Irina Hashmi, Bahar Akbal, Nurit Haspel, and Amarda Shehu "Protein Docking with Information on Evolutionary Conserved Interfaces" Computational Structural Biology Workshop (CSBW), pg. 358-365, Atlanta, GA, 2011.

Protein-protein structural assemblies modeled through the efforts described above have also been the subject of energetic refinement protocols detailed in 3) Bahar Aklbal-Delibas, Irina Hashmi, Amarda Shehu, and Nurit Haspel. An Evolutionary Conservation Based Method for Re ning and Reranking Protein Complex Structures. J Bioinf and Comp Biol 2012, 10(3):1242008; and 4) Bahar Akbal, Irina Hashmi, Amarda Shehu, and Nurit Haspel. "Refinement of Docked Protein Complex Structures Using Evolutionary Traces." Comp Struct Biol Workshop (CSBW), pg. 400-404, Atlanta, GA, 2011.

Recent efforts have focused on better identification and/or ranking of putative interaction interfaces in the context of evolutionary search algorithmic frameworks. An algorithm based on the Basin Hopping framework, shown effective and promising for modeling protein-protein dimers, is described in 5) Irina Hashmi and Amarda Shehu. "A Basin Hopping Algorithm for Protein-protein Docking." IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), pg. 466-469, Philadelphia, PA, 2012. An extended version of this work is in: 6) Irina Hashmi and Amarda Shehu. "HopDock: A Probabilistic Search Algorithm for Decoy Sampling in Protein-protein Docking." Proteome Science, 2013. A machine learning model to rapidly rank contact interfaces is integrated in the search in: 7) Irina Hashmi and Amarda Shehu. "Informatics-driven Protein-protein Docking." ACM BCBW - Comput Struct Biol Workshop (CSBW), Washington, D.C., 2013. A journal article on this line of work is expected to appear soon.

Irina's presentation at BIBM 2012.

On this Project:

  • Irina Hashmi

    Bahar Akbal-Delibas (UMass Boston)

    Nurit Haspel (Umass Boston)

    Amarda Shehu