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Title: 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.

 
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NSF-PAR ID:
10363520
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
Volume:
38
Issue:
6
ISSN:
1367-4803
Page Range / eLocation ID:
p. 1754-1755
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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