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I-TASSER D-I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK D-QUARK DRfold DRfold2 LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM DMFold SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA DeepMSA2 FASPR EM-Refiner GPU-I-TASSER

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14

GPU-I-TASSER
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

  • Reference:
    • 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).

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