Docking with QM/MM methods often improves the accuracy of the calculation substantially, and designing of a transition state analogue as enzyme inhibitor implies the determination of the transition state of the original ligand which is only accessible by quantum mechanical computation .
The main problem with quantum mechanical calculations is it's computational cost...so, where can I find a place in Egypt equipped with super or high computational resources to do such computations in a reasonable time ?
Have you searched the pyramids? (I apologize for the joke. But that was the first thing that popped up in my head after reading the title to your question.)
You might indeed need to do high-level QM calculations to determine the transition state, but you can leverage this high-cost information (about the geometry, energetics and mechanism of the reaction in a model, uncatalyzed, reaction in solution) by subsequent series of low-cost empirical valence bond simulations of the enzymatic reaction with as many inhibitors as you like, e.g. using Q molecular dynamics software package: http://xray.bmc.uu.se/~aqwww/q/
In my experience, the bottleneck is NEVER the computational cost, but rather design/analysis/interpretation of the calculations.
Thank you Muhammad Hagras,
I also found this web site of Minia University
http://www.compchem.net/index.php
Thank you Martin Klvana,
maybe the pyramids is not a good suggestion because pharaohs would make the computations much more complicated and with serious errors since they didn't know about symmetry and chirality (This is a fact about your interesting joke http://www.messagetoeagle.com/baffling-depictions-of-pharaohs-and-gods-with-two-left-or-two-right-hands/) .
I went to GUC and there is no cluster there.There is one in faculty of Science, department of mathematics, Cairo University and another cluster in faculty of science, Minia University .
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