GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool.

ABSTRACT:

Motivation

Accurate and efficient predictions of protein structures play an important role in understanding their functions. Iterative Threading Assembly Refinement (I-TASSER) is one of the most successful and widely used protein structure prediction methods in the recent community-wide CASP experiments. Yet, the computational efficiency of I-TASSER is one of the limiting factors that prevent its application for large-scale structure modeling.

Results

We present I-TASSER for Graphics Processing Units (GPU-I-TASSER), a GPU accelerated I-TASSER protein structure prediction tool for fast and accurate protein structure prediction. Our implementation is based on OpenACC parallelization of the replica-exchange Monte Carlo simulations to enhance the speed of I-TASSER by extending its capabilities to the GPU architecture. On a benchmark dataset of 71 protein structures, GPU-I-TASSER achieves on average a 10× speedup with comparable structure prediction accuracy compared to the CPU version of the I-TASSER.

Availability and implementation

The complete source code for GPU-I-TASSER can be downloaded and used without restriction from https://zhanggroup.org/GPU-I-TASSER/.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: MacCarthy EA 

PROVIDER: S-EPMC8896630 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature