[gmx-users] Predict Physical Properties of Novel Proteins

Anthony Nash anthony.nash at dpag.ox.ac.uk
Sun Apr 22 22:19:24 CEST 2018

Years ago, the initial idea behind my PhD was to use MD to screen transmembrane protein sequence designs to decide whether to carry that sequence through to the experimental stage. I quickly learned (and my supervisors, surprisingly) that a well-thought-out Molecular Dynamics simulation can be just as time consuming (and sometimes more so) and fraught with just as many difficulties as the in vivo aspects to table top molecular biology (growing cells, cloning, expressing and performing a particular assay). Thus, using MD as a filter is quite bold. 

Dr Anthony Nash PhD MRSC
Postdoctoral Research Associate 
Department of Physiology, Anatomy & Genetics 
Oxford University

On 22/04/2018 20:53, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Academic Research" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ac.research at icloud.com> wrote:

    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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