IntFOLD protocols

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IntFOLD specifications

Information


Unique identifier OMICS_03619
Name IntFOLD
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence for the target protein. Users may optionally provide a name for their protein sequence, their email address and alternative 3D models of their protein, for direct comparison and quality assessment.
Output data The output is presented as a simple table that summarizes all prediction data graphically through thumbnail images of plots and annotated 3D models.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Liam J. McGuffin <>

Publications for IntFOLD

IntFOLD in pipelines

 (2)
2017
PMCID: 5662874
PMID: 29123523
DOI: 10.3389/fimmu.2017.01375

[…] the simple modular architecture research tool (smart), from the european molecular biology laboratory (embl) website (, ). finally, three-dimensional structure predictions were performed using the intfold integrated protein structure and function prediction server () and visualized with the pymol molecular graphics system, version 1.8 schrödinger, llc. the modfold quality assessment server […]

2012
PMCID: 3582587
PMID: 23231440
DOI: 10.1186/1471-2164-13-694

[…] their frequencies were recorded. finally, the best 3d models for the csep families with confident (medium to certain) structure predictions (families 5, 12, 21, 22 and 23) were downloaded from the intfold server. each model was then visually inspected and the residues that were found to be under positive selection were highlighted using pymol (http://www.pymol.org)., the individual amino acid […]


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IntFOLD in publications

 (18)
PMCID: 5753887
PMID: 29317803
DOI: 10.1177/1177932217747277

[…] (hordeum vulgare l.), rice (oryza sativa l.), and sorghum (sorghum bicolor l.) cwm genes were generated using r packages phangorn and ape. protein structures of these cwm genes were predicted using intfold server. amino acid sequences of cwm proteins were added as an input to the intfold server. these predicted protein structures were investigated for structural motifs using sa-mot server […]

PMCID: 5735551
PMID: 29258508
DOI: 10.1186/s12936-017-2140-1

[…] in kh2.1 which was in kh3 earlier. all the other 155 isolates completely overlaps with the clusters observed previously., models were built using four independent structure prediction servers, intfold [], phyre2 [], raptorx [] and lomets []. for each model, the top model from each of the four servers was analysed using modfoldclust2 [] and manually inspected, showing all models […]

PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] which has not allowed the predicted and observed monomers to align as well as they can be aligned when truncated., in the casp 12 experiment the mcguffin group predicted tertiary structures using intfold [,,,] and other server models, then subsequently the highest scoring submitted model was further refined using the refold [] procedure. the refold refinement pipeline consists of three main […]

PMCID: 5662874
PMID: 29123523
DOI: 10.3389/fimmu.2017.01375

[…] the simple modular architecture research tool (smart), from the european molecular biology laboratory (embl) website (, ). finally, three-dimensional structure predictions were performed using the intfold integrated protein structure and function prediction server () and visualized with the pymol molecular graphics system, version 1.8 schrödinger, llc. the modfold quality assessment server […]

PMCID: 5820171
PMID: 28975675
DOI: 10.1002/prot.25396

[…] predicted models. therefore, we looked for methods and servers that could predict holo sites well (supporting information section tables s4 and s7). predictions from servers multicom‐construct and intfold4 performed well for all six holo sites. these methods likely employed algorithms that benefited from ligand‐binding template information and for modeling., this iteration of casp received […]


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IntFOLD institution(s)
School of Biological Sciences, University of Reading, Reading, UK

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