$F^2$Dock: 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 .