F2Dock: fast Fourier protein-protein docking.

ABSTRACT: 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 exten

SUBMITTER: Bajaj C 

PROVIDER: S-EPMC3058388 | biostudies-literature | 2011 Jan-Mar

REPOSITORIES: biostudies-literature