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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 citations

 (361)
call_split

Ion–ion interactions in the denatured state contribute to the stabilization of CutA1 proteins

2018
Sci Rep
PMCID: 5955972
PMID: 29769700
DOI: 10.1038/s41598-018-25825-7
call_split See protocol

[…] l 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. Counter-io […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] ANNOTATOR and found that 35 out of the 77 SNPs are located in a functional domain of their proteins. The final criterion was to investigate whether the SNP affects protein structural stability using FoldX. Only 27 common SNPs were in a region with a known structure or high similarity to a known structure which allows us to do homology modeling and FoldX analysis. 17 of them returned significant r […]

call_split

Hsp90 shapes protein and RNA evolution to balance trade offs between protein stability and aggregation

2018
Nat Commun
PMCID: 5934419
PMID: 29725062
DOI: 10.1038/s41467-018-04203-x
call_split See protocol

[…] ations that increase the protein aggregation propensity, and mutations that significantly alter sequence hydrophobicity. The effect of all amino acid mutations on protein stability was predicted with FoldX (foldxsuite.crg.es) for poliovirus proteins P1 (PDB structure 2PLV), 3C (4DCD), and 3D (4NLR). The effect of amino acid mutations on protein aggregation propensity was predicted with Tango (tang […]

library_books

The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

2018
PLoS One
PMCID: 5919626
PMID: 29698417
DOI: 10.1371/journal.pone.0196135

[…] The ΔGunfold° on each model for each protein was estimated using the command line version of FoldX []. It is important to notice that the computed ΔGunfold° is not comparable in proteins of different size, therefore we computed the average ΔGunfold° per residue as: ΔGunfold°^=ΔGunfold°r(8) r […]

library_books

Exploration of the effect of sequence variations located inside the binding pocket of HIV 1 and HIV 2 proteases

2018
Sci Rep
PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] the 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 (PDB […]

call_split

An antibody with Fab constant domains exchanged for a pair of CH3 domains

2018
PLoS One
PMCID: 5891013
PMID: 29630643
DOI: 10.1371/journal.pone.0195442
call_split See protocol

[…] y 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 TR […]

Citations

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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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