Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.

ABSTRACT: Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance (NMR) spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due to the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that serial code refactoring and parallel acceleration brought down the time taken of the software runni

SUBMITTER: Wright E 

PROVIDER: S-EPMC7250467 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature