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 <>

FoldX article

FoldX citations

 (6)
2017
PMCID: 5397141

[…] sequences were generated using the crystal structure of kyp in complex with mcphph dna and the h3 (1-15) peptide [pdb:4qeo] (6) as a starting model. changes in the dna sequence were made using the foldx software (24,25). models were energy minimized and equilibrated using the gromacs package (26) with the charmm36 force fields (27–29). the initial shortest distance between the protein […]

2014
PMCID: 4106229

[…] to its relative binding free energy. to compare the relative binding affinities of the gd-receptor complexes, we calculated the relative binding free energies for these complexes using the foldx program [55-57]. foldx uses a full atomic description of the structure of the proteins. the different energy terms taken into account in foldx have been weighted using empirical data obtained […]

2014
PMCID: 4026576

[…] pipeline to predict the disease-associated single amino acid polymorphism and takes an extensive list of molecular features into account. in this study we used its intermediate feature matrix., foldx [30] (http://foldx.crg.es/) was used to estimate protein stability based on energy change., popmusic [31] (http://babylone.ulb.ac.be/popmusic) was used to estimate protein stability and solvent […]

2014
PMCID: 3985714

[…] the repairpdb module applied to the minimized structures. we choose the first foldx protocol for comparison as it gave us better correlation with experimental values. to calculate binding energy by foldx, we used eq 2 and calculated the unfolding free energy of the whole complex and each monomer separately., the second method, beatmusic21 is specifically trained to calculate the change […]

2013
PMCID: 3812052

[…] steric overlaps. the parameters f1–9 were trained by maximizing the correlation between the calculated and experimental free-energy changes on a set of experimental residue mutants. the detail of foldx potential design and parameterization can be found in refs [53], [83]. we used the default parameters for the foldx calculation, except for the van der waal weight f1 which was increased […]

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

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