Parallelized protein folding on GPUs
GPU-I-TASSER is a GPU parallelization and performance analysis of protein structure prediction method, I-TASSER
(Iterative Threading Assembly Refinement), the first ranked automated server for protein structure prediction, according to Critical Assessment of Structure Prediction (CASP) experiments, CASP7 through CASP13. In particular, we aim at improving the performance by porting compute intensive operations to the GPU. Our implementation is based on OpenACC parallelization of the bottleneck replica-exchange Monte Carlo simulation of the program by keeping to a minimum the modifications of the existing CPU code while enhancing the speed and extending its capabilities to the GPU architecture.
Due to hardware limit, we are unable to provide an online server for GPU-I-TASSER. To use GPU-I-TASSER, please download the standalone package below:
Standalone GPU-I-TASSER package: GPU-I-TASSER1.0.tar.bz2
Instruction on using GPU-I-TASSER: GPU-ITASSER_README.txt
Benchmark dataset: dataset.tar.bz2
Elijah A MacCarthy, Chengxin Zhang, Yang Zhang and Dukka KC (2021)
GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool.
Bioinformatics, 38: 1754-1755 (2021).