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.
| Original language | English |
|---|---|
| Pages (from-to) | 1754-1755 |
| Number of pages | 2 |
| Journal | Bioinformatics |
| Volume | 38 |
| Issue number | 6 |
| DOIs | |
| State | Published - Mar 15 2022 |
| Externally published | Yes |
Funding
This work was supported in part by the National Science Foundation [DBI1564606 to D.K., IIS1901191, DBI2030790, MTM2025426 to Y.Z.]; the National Institute of General Medical Sciences [GM136422, S10OD026825 to Y.Z.] and the National Institute of Allergy and Infectious Diseases [AI134678 to Y.Z.].