Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms.

ABSTRACT: Fast Fourier transform (FFT)-based protein ligand docking together with parallel simulated annealing for both rigid and flexible receptor docking are implemented on graphical processing unit (GPU) accelerated platforms to significantly enhance the throughput of the CDOCKER and flexible CDOCKER - the docking algorithms in the CHARMM program for biomolecule modeling. The FFT-based approach for docking, first applied in protein-protein docking to efficiently search for the binding position and orientation of proteins, is adapted here to search ligand translational and rotational spaces given a ligand conformation in protein-ligand docking. Running on GPUs, our implementation of FFT docking in CDOCKER achieves a 15 000 fold speedup in the ligand translational and rotational space search in pro

SUBMITTER: Ding X 

PROVIDER: S-EPMC7495732 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature