On 10-2-2016 17:16, Ethan Merritt wrote:
> On Wednesday, 10 February 2016 07:54:28 AM sreetama das wrote:
>> Dear All,
>> I would like to compare the flexibility of the secondary structure elements forming the active site in homologous proteins. What are the possible methods of doing it? Not all the homologs have high sequence similarity (<50% similarity).
>
Obviously, the thing to do is MD. And, obviously, the thing to avoid is MD.
MD, if perfect, and a bit fast would be your method of choice, but MD
takes for ever, is not perfect, and you spend weeks and weeks learning
how to use GROMACS, NAMD, etc (unless you use YASARA-MD, but that costs
a bit of money).
Bert de Groot (http://www3.mpibpc.mpg.de/groups/de_groot/bgroot.html)
has written the software CONCOORD that predicts the outcome of MD
simulations. CONCOORD is orders of magnitude faster than MD softwares,
and for the kind of thing you are asking essentially just as good.
Greetings
Gert
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