[gmx-users] Predict Physical Properties of Novel Proteins

Academic Research ac.research at icloud.com
Sun Apr 22 21:53:28 CEST 2018

Hello Everyone,

I am computationally designing proteins, and I would like to ask if it is possible to simulate the physical properties of these proteins on gromacs in an attempt to filter the bad proteins from the good proteins, which I would then use to spend money/energy on expressing/purifying etc...

I am not looking for folding simulations since I already have another system for that.

First of all, can molecular dynamics be used to predict the physical properties of proteins? If not accurately, then at least allow me to differentiate between horrible proteins (very low stability) from proteins that are more likely to be stable in solution?

Second, other than Rg, RMSD, aggregation in solution, and thermostability, what other useful physical properties can gromacs measure out of a simulation? crystilisability?

I have successfully gone through the Lysozyme in Water tutorial prepared by the Bevan Lab. Being new to gromacs, and simulating totally novel proteins, would the parameters in that tutorial be a standard in simulating water soluble globular proteins? would they need just some tweaking? or should I start the parameters from scratch?


AC Research

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