On 3/29/13 7:16 AM, zalikha_ibrahim wrote:
Thanks f your reply, Dr.
I wanted to do PCA analysis on this x-ray structures compilation. Does that
mean I need to pretreat (i.e. fixing missing residues) those PDBs before
compiling it?
Yes, or otherwise analyze a subset of atoms that corresponds to some common
portion of all the proteins. If you insert missing residues, then they have
artificial positions; this may flaw your analysis. Actual simulations may be
better than just hacking together a bunch of incomplete X-ray structures.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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