Software and Data
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 now implemented in GROMACS-4.5.3.
Watch the video about a graphene sheet broken by an AFM tip here!
In a number of projects, FDA also helped to reveal the mechanism of allostery in proteins. More details are given here.
The FDA code can be downloaded from the FDA-GitHub repository
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.
Tcl procedure to quantify pre-stress in S-S bonds
The script identifies the S-S bonds in any protein considering that these information are supplied in the pdb file loaded in vmd. These information need to comply the format normally used in PDB files to described the presence of disulphide 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.