Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.

ABSTRACT: Energy evaluation using fast Fourier transforms (FFTs) enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods, efficient acceleration is achieved only in either the translational or the rotational subspace. Developing an efficient and accurate docking method that expands FFT-based sampling to five rotational coordinates is an extensively studied but still unsolved problem. The algorithm presented here retains the accuracy of earlier methods but yields at least 10-fold speedup. The improvement is due to two innovations. First, the search space is treated as the product manifold [Formula: see text], where [Formula: see text] is the rotation group representing the space of the rotating ligand, and [Formula:

SUBMITTER: Padhorny D 

PROVIDER: S-EPMC4968711 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature