Software and Data

Redox potential of a protein disuflide bond

Predicting the redox potential of a protein disuflide bond is very useful in various fields, from redox biochemistry to protein allostery to covalent ligand binding to cysteines. We explain in great detail, how you can run Molecular Dynamics simulations in Gromacs such that you obtain the disulfide bond redox potential of interest. Please find all…

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Tcl procedure to quantify pre-stress in S-S bonds

Here you will find a tcl script that contains a procedure able to calculate the properties of S-S bonds as defined by Schmidt et al. published in “Biochemistry (2006) Vol. 45 pp. 7429-7433. The script identifies the S-S bonds in any protein considering that these information are supplied in the pdb file loaded in vmd. These…

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Force distribution analysis (FDA)

Force distribution analysis (FDA) is a method to detect and follow force and stress propagation in proteins, reminiscent of Finite Element Analysis used to engineer macroscopic structures. The method is based on Molecular Dynamics simulations during which we directly calculate forces between each atom pair in a system. The most recent version of FDA is…

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Isopeptide bonds

The files relative to the work from B. Wang et al. (2013). Isopeptide bonds mechanically stabilize spy0128 in bacterial pili. Biophys J (2013)104(9):2051-7.