F2Dock: fast Fourier protein-protein docking.
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 F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, F2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .
Computational Visualization Center, Department of Computer Sciences and the Institute of Computational Engineering and Sciences, University of Texas at Austin, 1 University Station C0500, Austin, Texas 78712, USA. bajaj@cs.utexas.edu
Chandrajit
C
Bajaj
Rezaul
R
Chowdhury
Vinay
V
Siddavanahalli
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002417:Cattle; D019295:Computational Biology / Q000379:methods*; D005583:Fourier Analysis; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D055672:Static Electricity
D001426:Bacterial Proteins; D011506:Proteins