ModFOLD protocols

View ModFOLD computational protocol

ModFOLD statistics

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ModFOLD specifications

Information


Unique identifier OMICS_11951
Name ModFOLD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Single or multiple PDB files
Operating system Unix/Linux
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Liam J. McGuffin <>

Publications for ModFOLD

ModFOLD in pipelines

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

[…] 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 (version 4.0) was used to check the accuracy of the models ()., the genes encoding zebrafish caiap (nm_001025492), caiapδcard (deletion from i12 to y97), wild-type […]

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

[…] automated methods for fold recognition (intfold-ts), domain prediction (domfold), disorder prediction (disoclust), binding site residue predictions (funfold) and 3d model quality assessment (modfold) [,,]. for each protein, the pdb header files of the top structural templates were scanned for keywords referring to functions, such as rnase, ribonuclease and hydrolase, […]


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ModFOLD in publications

 (23)
PMCID: 5793430
PMID: 29390964
DOI: 10.1186/s12862-018-1129-x

[…] to evaluate the effect of mutations at conserved sites, and to localize the amino acid residues found to be under functional divergence by diverge v3.0. the quality of the model was assessed with modfold v4.0 []., the high quality and completeness of several platyhelminthes genomes (e.g. echinococcus spp., schistosoma mansoni) [, ], together with the criteria for the search for orthologs (see […]

PMCID: 5796147
PMID: 29315236
DOI: 10.3390/ijms19010198

[…] descent (ccd) module [], implemented in the computer program rosetta 3.1 [], was used to generate 1000 templates from hpv16 e6, which were ranked by a score function using the computer programs modfold [] and qmean []. the top 20 modeled structures (the 10 highest scores sorted by each scoring function without redundancy) were evaluated by mqaps and visual inspection. in order to obtain […]

PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] to a more manageable number and processed manually to determine the highest quality predicted pose., although many different forms of tertiary model evaluation exist; such as those implemented in modfold6 [], proq3 [,] and others [], recent progression onto quaternary protein modelling means that a reliable generic quaternary structure model quality assessment method has yet to be developed. […]

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

[…] 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 (version 4.0) was used to check the accuracy of the models ()., the genes encoding zebrafish caiap (nm_001025492), caiapδcard (deletion from i12 to y97), wild-type […]

PMCID: 5587760
PMID: 28878230
DOI: 10.1038/s41598-017-10932-8

[…] revealed that the most conserved amino acids located in the c-terminus of the protein (supplementary figure )., the three-dimensional model of mesoamp was created using modeller and validated using modfold that demonstrated that there was less than a 1:1,000 chance that the models were incorrect. the ramachandran plots for the models revealed a relatively high number of amino acids in allowed […]


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ModFOLD institution(s)
School of Biological Sciences, University of Reading, Whiteknights, UK
ModFOLD funding source(s)
This work was supported by an RCUK Academic Fellowship.

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