Deformation Energies from MD Trajectories

[Shahryar Alavi]

Dear Bio3D developers,

Intrinsically disordered peptides (IDPs) regulate many important cellular functions (a mini-review can be find here: https://doi.org/10.1073/pnas.0807977105) and MD simulations provide a useful tool to study these flexible structures. There are some web-tools to predict IDPs based on their sequence (e.g. http://iupred.enzim.hu/ and http://prdos.hgc.jp/cgi-bin/top.cgi). However, I think providing a function like deformation.nma() for MD trajectories could provide an insightful tool to dynamically consider IDPs.

Indeed, I don't know if it's possible to calculate deformation energies from an MD trajectory. I would appreciate any comments you might have.

[Barry Grant]

Thanks for the comments. We will add this to the 'to do list' and see if anyone bites.