Hi Acoot,
> Will you please suggest by which parameter we can use to describe the
> space (or deviation) a helix can move?
>
> As for helices 5- 10 can move in a rather larger space in comparison with
> helicex 1-4, does this mear helices 5-10 have much important biological
> function? What is your opinion?
well, these are fairly tricky research questions for which there is no
clear answer (especially without knowing about your project). There are a
lot of tools in Amber to understand protein structure and dynamics, such
as rmsd measurements, correlation analysis, PCA, etc. Maybe a good start
is to replicate the kind of analysis that people have conducted on similar
systems, asking similar questions to yours. One way or another, this takes
a good bit of preparatory work to become proficient in the analysis
methods...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Jun 24 2012 - 11:00:02 PDT
