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Protocols

I-TASSER specifications

Information


Unique identifier OMICS_08046
Name I-TASSER
Alternative name Iterative Threading ASSEmbly Refinement
Interface Web user interface
Restrictions to use None
Input data The primary amino acid sequence of the query protein.
Input format FASTA
Output data A summary of the submitted sequence and local structural feature prediction, the top 10 threading templates used, the top-ranked 3D structure models with global and local accuracy estimations, the top 10 proteins with similar structures to the query and structure-based function annotations on ligand-binding site, EC number and GO term.
Computer skills Basic
Version 4.3
Stability Stable
Requirements
COACH, COFACTOR, LOMET, SPICKER, ModRefiner,
Maintained Yes

Subtools


  • EC number & GO term prediction
  • MUSTER
  • S-SITE
  • TM-SITE

Maintainers


  • person_outline Yang Zhang <>
  • person_outline Jianyi Yang <>

Information


Unique identifier OMICS_08046
Name I-TASSER
Alternative name Iterative Threading ASSEmbly Refinement
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Version 5.1
Stability Stable
Registration required Yes

Subtools


  • EC number & GO term prediction
  • MUSTER
  • S-SITE
  • TM-SITE

Versioning


No version available

Maintainers


This tool is not maintained anymore.

Publications for Iterative Threading ASSEmbly Refinement

I-TASSER citations

 (1258)
library_books

Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6

2018
PMCID: 5930436
PMID: 29716651
DOI: 10.1186/s12964-018-0231-4

[…] was built using homology modelling. protein blast in eukaryotic genomes was carried out to analyse the sequence homology and identity. homology modelling of alpha tubulin was carried out by i-tasser, an online webserver for protein structure prediction and structure-based function annotation []. the tertiary structure prediction was performed by i-tasser server by using the best align […]

library_books

CHRNE compound heterozygous mutations in congenital myasthenic syndrome

2018
PMCID: 5944527
PMID: 29702980
DOI: 10.1097/MD.0000000000010347

[…] of c.442t>a (exon 5) were found in chrne. both mutations localized in conserved sequences. the c.442t>a (p.c148s) missense mutation in chrne was predicted to be damaging/deleterious. the iterative threading assembly refinement (i-tasser) server generated vastly different 3-dimensional (3d) atomic models based on protein sequences from wide-type and novel nonsense mutation […]

library_books

Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

2018
PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] crystal structure (1y6k; 22-235 residues) of native il10ra, we generated 13 full-length (1-578 residues) template-based models (one wild-type and 12 mutant models), by using swiss model-expasy and i-tasser web servers. consequently protein-protein interaction analysis and molecular docking of selected mutant (localized to the extracellular region) and native models of il10ra with its ligand […]

library_books

Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling

2018
PMCID: 5924475
PMID: 29703146
DOI: 10.1186/s12864-018-4685-y

[…] and the pfam domain database using smart software []. motifs were predicted by meme (meme-suite.org). the three-dimensional structure of the scamk protein was de novo modeled using the online i-tasser server []. protein-ligand docking was modeled relying on online server swissdock []., the transcriptome sequences and the expression value of all the protein-coding genes trypanosoma brucei […]

library_books

Interaction of the GntR family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 6803

2018
PMCID: 5923263
PMID: 29703909
DOI: 10.1038/s41598-018-25077-5

[…] the sll1961-trxm complex is summarized in supplementary fig.  and described in detail in supplementary text and supplementary table . three-dimensional structure predictions were performed using the i-tasser server. docking predictions were performed using the zdock server. foldit standalone was used for manual refinement of predicted structures., , electronic supplementary material , […]

library_books

Heterosubtypic immunity increases infectious dose required to infect Mallard ducks with Influenza A virus

2018
PMCID: 5919434
PMID: 29698449
DOI: 10.1371/journal.pone.0196394

[…] amino acid distance matrix was obtained by using geneious version 8.1.9 (biomatters ltd; auckland, new zealand)., amino acid sequences obtained from genbank were subjected to homology modeling using i-tasser []. the signal peptide (amino acid positions 1–18) were removed from the sequences submitted to the i-tasser server. pymol was then used to visualize molecular structures []. continuous […]


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I-TASSER institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

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