An Adaptive Irregularly Spaced Fourier Method for Protein-Protein Docking

In this paper we introduce a grid free irregularly sampled Fourier approach for accurately predicting rigid body protein-protein docking sites. Of the many docking approaches, grid based Fast Fourier Transform (FFT) approaches have been shown to produce by far the fastest, correlation profiles of complex protein-protein interactions over the six dimensional search space. However, these uniform sampling methods still possess high time complexity, and in particular, are highly memory intensive for predicting large protein-protein docking sites. By taking advantage of an irregularly and adaptively sampled, smooth particle representation of molecular shape, in combination with the use of irregularly spaced FFT transforms, we eliminate an explicit uniform grid. We are able to produce efficiently, highly compressed, but accurate, docking correlation profiles. This work was supported in part by NSF grants ACI-0220037, EIA-0325550, and NIH grants 0P20 RR020647, and R01 GM074258 [email protected] [email protected] [email protected]