We Need Collaboration: Our human molecular biology group recently performed CYP17 gene polymorphism association with Polycystic Ovarian Syndrome in number of patients (Paper write up has been completed up to that). We are interested to find out the Influence of Single Nucleotide Polymorphisms in Cytochrome P17 on Substrate Recognition Using Computational Docking and Molecular Dynamics Simulation. For this work I need some expert having command on Amber10/Gromacs. I'm interested to perform 20ns MD simulation and then see the effect of docking between CYP17 (Wild-type and mutants) and its inhibitor. If you are interested to perform this analysis. please contact me. (Authorship will be granted).
We are supposed to submit the paper in the month of February. Thanks
Assumption that 20ns may be enough is really risky - it's not that huge system to limit the simulation time to so short time, and at the same time it's not that small to expect that comparison of such a short MDs will give interesting results. I'm also not sure if good quality structures are available (but honestly I didn't have time to check it).
Anyway - good luck :]
I think that it would be really good for people that would like to try to help you to know how many mutations are you planning to work with. As Rafal said, 20 ns doesn't seem to be really long to evaluate substrate recognition or binding stability, but if you are planning to test 10 mutants, then you might be short in real time, since that would already be 200 ns of simulations, and you need at least a few repetitions in order to get some error estimations of whatever the outcome of those simulations you get. Getting that for february might be too hard even for the skilled computational biologist if computational resources are limiting and meaningful conclusions are not as straightforward as you expect.
Dear Usman Mirza
We have good computational resources and 20ns takes about 4 days fir normal and medium simulation system. Send your file to my e-mail address.
If you still need help or you want to try out some simulations, just let us know.
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