F3Dock: A Fast, Flexible and Fourier Based Approach to Protein-Protein Docking

Chandrajit Bajaj, Rezaul Alam Chowdhury, and Vinay Siddavanahalli

ICES Report 08-01
The University of Texas at Austin, Institute for Computational Engineering and Sciences (ICES), Report 08-01, January 2008 (Updated: April 2009), 27 pages


Protein interactions, key to many biological processes, involves induced fit between flexible proteins which typically undergo conformational changes. Modeling this flexible protein-protein docking is an important step in drug discovery, structure determination and understanding structure-function relationships. In this paper, we present F3Dock, a Fast Flexible and Fourier based docking algorithm which utilizes adaptive sampling of orientation and conformational spaces, and a hierarchical molecular flexibility and structure representation. Different conformations are adaptively sampled and docked using a Non-equispaced Fast Fourier based algorithm.

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