FoldX protocols

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FoldX specifications

Information


Unique identifier OMICS_00129
Name FoldX
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FoldX

Maintainer


  • person_outline Joost Schymkowitz <>

Publication for FoldX

FoldX in pipelines

 (10)
2017
PMCID: 5397141
PMID: 28053115
DOI: 10.1093/nar/gkw1330

[…] sequences were generated using the crystal structure of kyp in complex with mcphph dna and the h3 (1-15) peptide [pdb:4qeo] () as a starting model. changes in the dna sequence were made using the foldx software (,). models were energy minimized and equilibrated using the gromacs package () with the charmm36 force fields (–). the initial shortest distance between the protein and the box […]

2017
PMCID: 5531539
PMID: 28750054
DOI: 10.1371/journal.pone.0181490

[…] cutoff for non-bonded interactions. non-hydrogen atoms were restrained at their crystallographic positions with a harmonic force constant of 5 kcal/(mol.a2)., we used three protocols (sie-scwrl, foldx and rosetta) for modeling mutants and scoring their binding affinities. for each of these protocols, additional refinement of the amber-refined parent structure was carried out as prescribed […]

2017
PMCID: 5638407
PMID: 29023497
DOI: 10.1371/journal.pone.0186260

[…] with pdb:6pax as a template. the model was recombined with dna chains in 6pax by pymol (https://www.pymol.org) and the resulting pdb file was optimized with repairpdb of foldx (http://foldxsuite.crg.eu). the structure of the p20l variant was modeled using builtmodel of foldx. the stability of the pax9-dna complex was calculated with analysecomplex […]

2016
PMCID: 5019393
PMID: 27617746
DOI: 10.1371/journal.pone.0161837

[…] template. alignment of model to 2h2wa, as well as model visualization were performed in pymol []., changes in protein folding stabilities and protein-protein binding stabilities were estimated using foldx [,]. foldx was chosen for this study to balance accuracy and speed [,]. given the large number of substitutions studied here, it is not possible to use accurate statistical mechanical […]

2015
PMCID: 4669690
PMID: 25950479
DOI: 10.1038/cddis.2015.110

[…] cii (pdb id 1zoy, sequence identity 95, 96, 92, and 88% for sdha to sdhd) using the modeller suite of programs. the single point sdhc mutations (i56f, s68a, r72c) were then introduced using the foldx program, which was also used to optimize the side chain rotamers within the wt as well as mutated structures. all the structures were further subjected to a short (10 ns, implicit solvation) […]


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FoldX in publications

 (304)
PMCID: 5955972
PMID: 29769700
DOI: 10.1038/s41598-018-25825-7

[…] residues of the c subunit, were modeled in quanta2000 (accelrys) using the coordinates of n-terminal residues of the a subunit as a reference. the structures of ec0vv and ec0vv_6 were modeled using foldx, based on the structure of ec0sh. hydrogen atoms were added to each protein. the models were solvated in water boxes with a minimum distance of 1.2 nm between the protein and the box. […]

PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] later, we annotated whether a snp is located in any functional domain of the corresponding protein or not.4.5)average free energy change (ddg, kcal/mol) of the protein by the snp as predicted by foldx from 5 runs [] is significant i.e. more than 0.5 kcal/mol or less than − 0.5 kcal/mol. the menu option “mutate residue” in the foldx plugin for yasara [] was used to predict free energy changes […]

PMCID: 5934419
PMID: 29725062
DOI: 10.1038/s41467-018-04203-x

[…] to identify variants that differed significantly in their effect on protein stability or aggregation propensity across passages (fig. ). first, we used the experimentally-rooted and well-validated foldx approach– to calculate the effects of all possible single point mutations on protein stability in the three viral proteins for which crystal structures are available, the capsid p1, […]

PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] six substitutions occurring between pr1 and pr2 pockets (t31s, v32i, m46i, i47v, l76m, and v82i). for this purpose, we modelled 63 pr1 mutants containing one to six pocket substitutions using the foldx software. for each mutant, we built five mutant structures that lead to a set of 315 pr1 mutant structures (see material & methods). we compared the conformation of residue 45_b in one pr1 […]

PMCID: 5891013
PMID: 29630643
DOI: 10.1371/journal.pone.0195442

[…] in the regions of the newly created interface and of the residues connecting the variable and the constant domains, the constructed molecule was energy-minimized using the repairpdb function of the foldx software [] (version 3.0b6). potential mutations that could contribute to optimization of the novel variable and constant domain interface were identified by visual inspection of the modelled […]


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FoldX institution(s)
Switch Laboratory, Flanders Interuniversity Institute for Biotechnology (VIB), Vrije Universiteit Brussel, Pleinlaan 2,Brussel, Belgium

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