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Issue No. 01 - January-February (2011 vol. 8)
ISSN: 1545-5963
pp: 45-58
Chandrajit Bajaj , University of Texas at Austin, Austin
Rezaul Chowdhury , University of Texas at Austin, Austin
Vinay Siddavanahalli , Google Inc., Mountain View
The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code {\rm F}^2Dock (F^2= {\rm \underline{F}ast \underline{F}ourier}). We have calibrated {\rm F}^2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that {\rm F}^2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, {\rm F}^2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .
Computational structural biology, protein-protein interactions, fast Fourier transform, algorithms, docking, redocking.

C. Bajaj, V. Siddavanahalli and R. Chowdhury, "$F^2$Dock: Fast Fourier Protein-Protein Docking," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 45-58, 2009.
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