ahmet yıldırım wrote:
Dear Justin,
can you suggest me published paper related to about hydrophobic and
hydrophilic contacts?
A few minutes on Google or the literature searching database of your choice
should turn up something useful. If you need to understand the definition or
nature of such interactions, a basic biochemistry textbook should cover it.
-Justin
03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
ahmet yıldırım wrote:
Dear Justin,
You said before "you can obtain some idea by using g_mindist to
calculate hydrophobic and hydrophilic contacts between the
protein and ligand".
That is, I can explore whether there is hydrophobic or
hydrophilic feature of ligand using g_mindist tool. is this correct?
I did the calculations related to protein_ligand interactions
(protein contains two ligand). I plotted the graphs of distance
and numcount versus simulation time for each ligand. The number
of contacts in ligand x is more than the other ligand y. Which
of this ligands are hydrophobic? Which is hydrophilic? I know
you are not private tutor. Please don't be angry :(
I certainly hope I haven't given the impression that I'm some angry
tyrant. I'm happy to answer reasonable questions across the list,
time permitting.
To obtain information about hydrophobic and hydrophilic contacts,
you need to use special index groups that tell g_mindist (or any
other tool) which atoms to consider. In this way, you can count how
many of each type of contact evolve over time.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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Ahmet YILDIRIM
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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