Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology.

ABSTRACT: Protein docking methods are powerful computational tools to study protein-protein interactions (PPI). While a significant number of docking algorithms have been developed, they are usually based on rigid protein models or with limited considerations of protein flexibility and the desolvation effect is rarely considered in docking energy functions, which may lower the accuracy of the predictions. To address these issues, we introduce a PPI energy function based on the site-identification by ligand competitive saturation (SILCS) framework and utilize the fast Fourier transform (FFT) correlation approach. The free energy content of the SILCS FragMaps represent an alternative to traditional energy grids and they can be efficiently utilized to guide FFT-based protein docking. Application of the

SUBMITTER: Yu W 

PROVIDER: S-EPMC6408985 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature