[gmx-users] Interaction energy graph

Justin Lemkul jalemkul at vt.edu
Sun Mar 16 15:06:37 CET 2014

On 3/16/14, 12:49 AM, kannan wrote:
> Dear Justin,
> sorry sir i forget to attahc the files, it is here attached. Thank you very
> much for your reply.. I answer the above question,
> 1. I am doing the protein-ligand interaction(electrostati+vanderWaals). I
> took the 140 amino acid as a sequence which contains binding site of the
> protein in Chain A of protein.
> 2. why i choose this sequence is, to know the binding interaction in deep.
> my objective is what are the amino acid residues are important for the
> interaction with ligand and if we dock the ligand far away from the
> important amino acid residues(which is essential for strong binding), how
> the interaction energy varies.
> 3. while docking ligand with important amino acid residue, i get the
> 'A-plot', where as if i dock the ligand far away from this particular amino
> acid residue, i get the 'B-plot'.
> I think, my conclusion is that, the decreasing interaction in the B-plot is
> due to the lack of the particular one important amino acid residue. so this
> particular residue and its region is has more contribution in the binding...
> I attached both the A-plot and B-plot sir...
> is my conclusion correct from the graph?

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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