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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 ●TCRfinder

●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

HPmod (Human Proteome Model) ory for human protein structure and function that automatically predicted by the state-of-the-art algorithm from Yang Zhang Lab. Protein structure models are predicted by D-I-TASSER, and the protein functions, including Gene Ontology (GO), Enzyme Commission (EC), and ligand-binding sites, are predicted by COFACTOR. The database contains 19,512 proteins collected from Uniprot, which can be classified as 12,236 single-domain proteins and 7,276 multi-domain proteins. (>>more about the HPmod database)

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HPmod News

The current database contains 19,512 entries.

Apr 30, 2022: 76 models for human complete genome proteins recently reported by science journal are generated by D-I-TASSER-AF2 modeling.

Apr 20, 2022: 1,689 models for proteins of human proteome are generated by D-I-TASSER-AF2 modeling. The distance prediction is created by AlphaFold2, AttentionPotential and DeepPotential, the initial conformations are from AlphaFold2 models and LOMETS3 templates, then a Replica-Exchange Montre Carlo simulation is used for constructing models. Multi-domain protein is first spilt by FUpred to domain-level sequences, individual domain models are predicted by D-I-TASSER-AF2 modeling pipeline, then the first D-I-TASSER-AF2 domain-level models are assembled by DeepDEMO to a full-length model.

Sep 1, 2021: 19,512 models for proteins of human proteome are generated by full D-I-TASSER modeling. The distance prediction is created by AttentionPotential and DeepPotential, and initial conformations are from LOMETS3 templates, then a Replica-Exchange Montre Carlo simulation is used for constructing 5 models. Multi-domain protein is first spilt by FUpred to domain-level sequences, individual domain models are predicted by D-I-TASSER modeling pipeline, then the first D-I-TASSER domain-level models are assembled by DeepDEMO to a full-length model.

May 1, 2021: 19,326 models for proteins of human proteome are generated by D-I-TASSER ab initio modeling. The distance prediction is created by DeepPotential, then a L-BFGS system is used for constructing 10 initial models. Those initial models are then refined by D-I-TASSER to generate 5 models. Multi-domain protein is first spilt by FUpred to domain-level sequences, individual domain models are predicted by D-I-TASSER ab initial pipeline, then be assembled by DEMO to a full-length model.

References

Wei Zheng, Yang Li, Qiqige Wuyun, Xiaogen Zhou, Chengxin Zhang, Robin Pearce, Eric W. Bell, Yiheng Zhu, Yang Zhang. Integrating deep neural network models with I-TASSER for accurate protein structure prediction. Submitted. (2021). [PDF] [Support Information] [Database]

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