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
Gene Ontology (GO) terms and the confidence score
Ligand-binding sites and the confidence score
An image of the predicted ligand-binding sites
Standalone Suiteedit
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.
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 at README.txt.
Referencesedit
^ abRoy A, Kucukural A, Zhang Y (2010). "I-TASSER: a unified platform for automated protein structure and function prediction". Nature Protocols. 5 (4): 725–738. doi:10.1038/nprot.2010.5. PMC2849174. PMID 20360767.
^Roy A, Yang J, Zhang Y (2012). "COFACTOR: An accurate comparative algorithm for structure-based protein function annotation". Nucleic Acids Research. 40 (Web Server issue): W471–W477. doi:10.1093/nar/gks372. PMC3394312. PMID 22570420.
^Zhang C, Freddolino PL, Zhang Y (2017). "COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information". Nucleic Acids Research. 45 (W1): W291–W299. doi:10.1093/nar/gkx366. PMC5793808. PMID 28472402.
^Moult, J; et al. (1995). "A large-scale experiment to assess protein structure prediction methods" (PDF). Proteins. 23 (3): ii–iv. doi:10.1002/prot.340230303. PMID 8710822.
^Battey, JN; et al. (2007). "Automated server predictions in CASP7". Proteins. 69 (Suppl 8): 68–82. doi:10.1002/prot.21761. PMID 17894354.
^Wu S, Zhang Y (2007). "LOMETS: A local meta-threading-server for protein structure prediction". Nucleic Acids Research. 35 (10): 3375–3382. doi:10.1093/nar/gkm251. PMC1904280. PMID 17478507.
^Swendsen RH, Wang JS (1986). "Replica Monte Carlo simulation of spin glasses". Physical Review Letters. 57 (21): 2607–2609. doi:10.1103/physrevlett.57.2607. PMID 10033814.
^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. PMID 15011258.
^Zhang J, Liang Y, Zhang Y (2011). "Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling". Structure. 19 (12): 1784–1795. doi:10.1016/j.str.2011.09.022. PMC3240822. PMID 22153501.
^Xu D, Zhang Y (2011). "Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization". Biophysical Journal. 101 (10): 2525–2534. doi:10.1016/j.bpj.2011.10.024. PMC3218324. PMID 22098752.
^Yang J, Roy A, Zhang Y (2013). "Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment". Bioinformatics. 29 (20): 2588–2595. doi:10.1093/bioinformatics/btt447. PMC3789548. PMID 23975762.
^Yang J, Roy A, Zhang Y (2015). "The I-TASSER Suite: Protein structure and function prediction". Nature Methods. 12 (1): 7–8. doi:10.1038/nmeth.3213. PMC4428668. PMID 25549265.
External linksedit
I-TASSER server homepage
The Yang Zhang Lab
CASP homepage
How to use on-line I-TASSER server for protein structure and function prediction
December 15, 2023
tasser, iterative, threading, assembly, refinement, bioinformatics, method, predicting, three, dimensional, structure, model, protein, molecules, from, amino, acid, sequences, detects, structure, templates, from, protein, data, bank, technique, called, fold, r. I TASSER Iterative Threading ASSEmbly Refinement is a bioinformatics method for predicting three dimensional structure model of protein molecules from amino acid sequences 1 It detects structure templates from the Protein Data Bank by a technique called fold recognition or threading The full length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations I TASSER is one of the most successful protein structure prediction methods in the community wide CASP experiments I TASSERI TASSER pipeline for protein structure and function prediction Developer s Yang Zhang LabWebsitezhanglab wbr ccmb wbr med wbr umich wbr edu wbr I TASSER wbr I TASSER has been extended for structure based protein function predictions which provides annotations on ligand binding 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 Contents 1 Ranking in CASP 2 Method and pipeline 3 On line Server 4 Standalone Suite 5 References 6 External linksRanking in CASP editI 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 No 1 in CASP7 2006 5 No 1 in CASP8 2008 Official ranking of CASP8 164 targets No 2 in CASP9 2010 Official ranking of CASP9 147 targets No 1 in CASP10 2012 Official ranking of CASP10 127 targets No 1 in CASP11 2014 Official ranking of CASP11 126 targets No 1 in CASP12 2016 Official ranking of CASP12 96 targets No 1 in CASP13 2018 Official ranking of CASP13 112 targets No 1 in CASP14 2020 Official ranking of CASP14 96 targets Method and pipeline editI TASSER is a template based method for protein structure and function prediction 1 The pipeline consists of six consecutive steps 1 Secondary structure prediction by PSSpred 2 Template detection by LOMETS 6 3 Fragment structure assembly using replica exchange Monte Carlo simulation 7 4 Model selection by clustering structure decoys using SPICKER 8 5 Atomic level structure refinement by fragment guided molecular dynamics simulation FG MD 9 or ModRefiner 10 6 Structure based biology function annotation by COACH 11 On line Server editThis section does not cite any sources Please help improve this section by adding citations to reliable sources Unsourced material may be challenged and removed December 2021 Learn how and when to remove this template message 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 editThe 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 amp 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 at README txt References edit a b Roy A Kucukural A Zhang Y 2010 I TASSER a unified platform for automated protein structure and function prediction Nature Protocols 5 4 725 738 doi 10 1038 nprot 2010 5 PMC 2849174 PMID 20360767 Roy A Yang J Zhang Y 2012 COFACTOR An accurate comparative algorithm for structure based protein function annotation Nucleic Acids Research 40 Web Server issue W471 W477 doi 10 1093 nar gks372 PMC 3394312 PMID 22570420 Zhang C Freddolino PL Zhang Y 2017 COFACTOR improved protein function prediction by combining structure sequence and protein protein interaction information Nucleic Acids Research 45 W1 W291 W299 doi 10 1093 nar gkx366 PMC 5793808 PMID 28472402 Moult J et al 1995 A large scale experiment to assess protein structure prediction methods PDF Proteins 23 3 ii iv doi 10 1002 prot 340230303 PMID 8710822 Battey JN et al 2007 Automated server predictions in CASP7 Proteins 69 Suppl 8 68 82 doi 10 1002 prot 21761 PMID 17894354 Wu S Zhang Y 2007 LOMETS A local meta threading server for protein structure prediction Nucleic Acids Research 35 10 3375 3382 doi 10 1093 nar gkm251 PMC 1904280 PMID 17478507 Swendsen RH Wang JS 1986 Replica Monte Carlo simulation of spin glasses Physical Review Letters 57 21 2607 2609 doi 10 1103 physrevlett 57 2607 PMID 10033814 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 PMID 15011258 Zhang J Liang Y Zhang Y 2011 Atomic Level Protein Structure Refinement Using Fragment Guided Molecular Dynamics Conformation Sampling Structure 19 12 1784 1795 doi 10 1016 j str 2011 09 022 PMC 3240822 PMID 22153501 Xu D Zhang Y 2011 Improving the Physical Realism and Structural Accuracy of Protein Models by a Two step Atomic level Energy Minimization Biophysical Journal 101 10 2525 2534 doi 10 1016 j bpj 2011 10 024 PMC 3218324 PMID 22098752 Yang J Roy A Zhang Y 2013 Protein ligand binding site recognition using complementary binding specific substructure comparison and sequence profile alignment Bioinformatics 29 20 2588 2595 doi 10 1093 bioinformatics btt447 PMC 3789548 PMID 23975762 Yang J Roy A Zhang Y 2015 The I TASSER Suite Protein structure and function prediction Nature Methods 12 1 7 8 doi 10 1038 nmeth 3213 PMC 4428668 PMID 25549265 External links editI TASSER server homepage The Yang Zhang Lab CASP homepage How to use on line I TASSER server for protein structure and function prediction Retrieved from https en wikipedia org w index php title I TASSER amp oldid 1149644505, wikipedia, wiki, book, books, library,
