I want to study thermal stability and structural transitions occurring in a protein over a range of temperatures say from 20 to 90C. Which tool can be used? Is there any online server? Or which module of Schrodinger can be useful? Anybody knows if there is any tutorial/scripts to use in Gromacs?
Dear Mr. Bendre,
You may predict the protein thermodynamic stability changes upon single-site mutations by these tools (https://soft.dezyme.com/). Pucci and co-workers described very nicely (https://www.nature.com/articles/srep23257.pdf).
You may also follow these articles (http://pubs.acs.org/doi/abs/10.1021/jp003602d and https://journals.iucr.org/f/issues/2016/02/00/en5571/en5571.pdf) for your better understanding.
Hope, these will be helpful for your research.
Thanks.
U can do Replica-Exchange Molecular Dynamics (REMD). U can use any software like gromacs for that. Or simply u can run multiple simulations with different temperatures.
Stability could be monitored using constant-T MD simulations at say 10 T values, or REMD using NAMD or Gromacs.
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