Ranking in CASP
I-TASSER (as 'Zhang-Server') has been consistently ranked as the top method in CASP, a community-wide experiment to benchmark the best structure prediction methods in the field ofMethod and pipeline
I-TASSER is a template-based method for protein structure and function prediction. The pipeline consists of six consecutive steps: *1, Secondary structure prediction bOn-line Server
The I-TASSER server allows users to generate automatically protein structure and function predictions. *Input **Mandatory: ***Amino acid sequence with length from 10 to 1,500 residues **Optional (user can provide optionally restraints and templates to assist I-TASSER modeling): ***Contact restraints ***Distance maps ***Inclusion of special templates ***Exclusion of special templates ***Secondary structures *Output **Structure prediction: ***Secondary structure prediction ***Solvent accessibility prediction ***Top 10 threading alignment from LOMETS ***Top 5 full-length atomic models (ranked based on cluster density) ***Top 10 proteins in PDB which are structurally closest to the predicted models ***Estimated accuracy of the predicted models (including a confidence score of all models, predicted TM-score and RMSD for the first model, and per-residue error of all models) ***B-factor estimation **Function prediction: ***Enzyme Classification (EC) and the confidence score ***Gene Ontology (GO) terms and the confidence score ***Ligand-binding sites and the confidence score ***An image of the predicted ligand-binding sitesStandalone Suite
The I-TASSER Suite is a downloadable package of standalone computer programs, developed by the Yang Zhang Lab for protein structure prediction and refinement, and structure-based protein function annotations. Through the I-TASSER License, researchers have access to the following standalone programs: *I-TASSER: A standalone I-TASSER package for protein 3D structure prediction and refinement. *COACH: A function annotation program based on COFACTOR, TM-SITE and S-SITE. *COFACTOR: A program for ligand-binding site, EC number & GO term prediction. *TM-SITE: A structure-based approach for ligand-binding site prediction. *S-SITE: A sequence-based approach for ligand-binding site prediction. *LOMETS: A set of locally installed threading programs for meta-server protein fold-recognition. *MUSTER: A threading program to identify templates from a non-redundant protein structure library. *SPICKER: A clustering program to identify near-native protein model from structure decoys. *HAAD: A program for quickly adding hydrogen atoms to protein heavy-atom structures. *EDTSurf: A program to construct triangulated surfaces of protein molecules. *ModRefiner: A program to construct and refine atomic-level protein models from C-alpha traces. *NW-align: A robust program for protein sequence-to-sequence alignments by Needleman-Wunsch algorithm. *PSSpred: A highly accurate program for protein secondary structure prediction. *Library: I-TASSER structural and functional template library weekly updated and freely accessible to the I-TASSER users. Help documents *Instruction on how to download and install the I-TASSER Suite can be found aReferences
{{reflist, refs= {{cite journal , vauthors=Roy A, Kucukural A, Zhang Y , year=2010 , title=I-TASSER: a unified platform for automated protein structure and function prediction , journal=Nature Protocols , volume=5 , issue=4 , pages=725–738 , doi=10.1038/nprot.2010.5 , pmid=20360767 , pmc=2849174 {{cite journal , vauthors=Roy A, Yang J, Zhang Y , year=2012 , title=COFACTOR: An accurate comparative algorithm for structure-based protein function annotation , journal=Nucleic Acids Research , volume=40 , issue=Web Server issue , pages=W471–W477 , doi=10.1093/nar/gks372 , pmid=22570420 , pmc=3394312 {{cite journal , vauthors=Zhang C, Freddolino PL, Zhang Y , year=2017 , title=COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information , journal=Nucleic Acids Research , volume=45 , issue=W1 , pages=W291–W299 , doi=10.1093/nar/gkx366 , pmid= 28472402, pmc=5793808 {{cite journal , vauthors=Zheng W, Wuyun Q, Li Y, Liu Q, Zhou X, Peng C, Zhu Y, Freddolino L, Zhang Y , year=2025 , title=Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER , journal=Nature Biotechnology , doi=10.1038/s41587-025-02654-4 , doi-access=free {{cite journal , author=Moult, J, year=1995 , title=A large-scale experiment to assess protein structure prediction methods , journal=Proteins , volume=23 , issue=3 , pages=ii–iv , doi=10.1002/prot.340230303, display-authors=etal , pmid=8710822, url=https://zenodo.org/record/1229334 {{cite journal , author=Battey, JN, year=2007 , title=Automated server predictions in CASP7 , journal=Proteins , volume=69 , issue=Suppl 8 , pages=68–82 , pmid=17894354 , doi=10.1002/prot.21761, display-authors=etal, doi-access=free {{cite journal , vauthors=Wu S, Zhang Y , year=2007 , title=LOMETS: A local meta-threading-server for protein structure prediction , journal=Nucleic Acids Research , volume=35 , issue=10 , pages=3375–3382 , pmid=17478507 , pmc=1904280 , doi=10.1093/nar/gkm251 {{cite journal , vauthors=Swendsen RH, Wang JS , year=1986 , title=Replica Monte Carlo simulation of spin glasses , journal=Physical Review Letters , volume=57 , issue=21 , pages=2607–2609 , pmid=10033814 , doi=10.1103/physrevlett.57.2607, bibcode=1986PhRvL..57.2607S {{cite journal , vauthors=Zhang Y, Skolnick J , year=2004 , title=SPICKER: A Clustering Approach to Identify Near-Native Protein Folds , journal=Journal of Computational Chemistry , volume=25 , pages=865–871 , pmid=15011258 , doi=10.1002/jcc.20011 , issue=6 {{cite journal , vauthors=Zhang J, Liang Y, Zhang Y , year=2011 , title=Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling , journal=Structure , volume=19 , issue=12 , pages=1784–1795 , pmid=22153501 , pmc=3240822 , doi=10.1016/j.str.2011.09.022 {{cite journal , vauthors=Xu D, Zhang Y , year=2011 , title=Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization , journal=Biophysical Journal , volume=101 , issue=10 , pages=2525–2534 , pmid=22098752 , pmc=3218324 , doi=10.1016/j.bpj.2011.10.024, bibcode=2011BpJ...101.2525X {{cite journal , vauthors=Yang J, Roy A, Zhang Y , year=2013 , title=Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment , journal=Bioinformatics , volume=29 , issue=20 , pages=2588–2595 , pmid=23975762 , pmc=3789548 , doi=10.1093/bioinformatics/btt447 {{cite journal , vauthors=Yang J, Roy A, Zhang Y , year=2015 , title=The I-TASSER Suite: Protein structure and function prediction , journal=Nature Methods , volume=12 , issue=1 , pages=7–8 , pmid=25549265 , pmc=4428668 , doi=10.1038/nmeth.3213External links