FoldX protocols

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)
2014
PMCID: 3985714
PMID: 24803870
DOI: 10.1021/ct401022c

[…] to reproduce the electrostatic free energy of the 20 amino acids in md simulations with explicit water molecules.56, we also estimated binding energy change using three independent methods. the foldx method19 calculates the effect of mutations on protein stability using an empirical force field. it optimizes the side chain configurations without taking into account the backbone […]

2014
PMCID: 3985714
PMID: 24803870
DOI: 10.1021/ct401022c

[…] stability using an empirical force field. it optimizes the side chain configurations without taking into account the backbone conformational movements. we tested two different protocols using foldx: the repairpdb module applied to protein crystal structures and the repairpdb module applied to the minimized structures. we choose the first foldx protocol for comparison as it gave us better […]

2014
PMCID: 3985714
PMID: 24803870
DOI: 10.1021/ct401022c

[…] movements. we tested two different protocols using foldx: the repairpdb module applied to protein crystal structures and 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 […]

2014
PMCID: 3985714
PMID: 24803870
DOI: 10.1021/ct401022c

[…] 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: 3693407
PMID: 23778582
DOI: 10.1038/tp.2013.49

[…] of 3dligandsite and the calcium coordination found in rabphilin-3a (pdb id: 2k3h). stabilities of wild-type and variant structures were compared by calculating difference binding energies δδg using foldx. dynamic structures were generated using the method of normal and geometric parameters that have been determined with dyndom.19 model structures were visualized using pymol […]

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

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