I-TASSER has been extended for structure-based protein function predictions, which provides annotations on ligandbinding site, gene ontology and enzyme commission by structurally matching structural models of the target protein to the known proteins in protein function databases.[2][3] It has an on-line server built in the Yang Zhang Lab at the University of Michigan, Ann Arbor, allowing users to submit sequences and obtain structure and function predictions. A standalone package of I-TASSER is available for download at the I-TASSER website.
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 of protein folding and protein structure prediction. CASP takes place every two years since 1994.[4]
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
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.[12] 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.
^Zhang Y, Skolnick J (2004). "SPICKER: A Clustering Approach to Identify Near-Native Protein Folds". Journal of Computational Chemistry. 25 (6): 865–871. doi:10.1002/jcc.20011. PMID15011258.
