Re: CCL:receptor flexibility in CADD

Please check this website for a study related to :
 http://www.hughesinstitute.org/pages/hiv_inhibitors.html
 Thanks,
 Anil.
 Heather A. Carlson wrote:
 > Hello All,
 >
 > We all know that it is a limitation to use a single protein structure
 > to represent a target site on a protein.  However, many of us still use
 > that approach as there is no accepted way of accommodating the inherent
 > flexibility of an active site in computer aided drug design.  There are
 > many means of accommodating ligand flexibility... I am interested in
 > receptor flexibility.
 >
 > I've recently developed a method for superimposing multiple protein
 > conformations to represent the inherent flexibility of a receptor when
 > developing a complementary pharmacophore model (an ASAP article is
 > available through J Phys Chem A: Carlson, Masukawa, McCammon).  The
 > only other work I have found that is at all similar is a ligand docking
 > study by Knegtel, Kuntz, and Oshiro (J Mol Biol 1997, 266, 424-440)
 > which introduces weighting methods either for the interaction energy
 > between a ligand and the receptor or in the description the geometry of
 > the site.
 >
 > Does anyone know of methods for accommodating an ensemble of protein
 > conformations?  Has anyone tried a similar idea without success or know
 > of particularly interesting cases where the lack of protein flexibility
 > leads to incorrect predictions?
 >
 > Thank you,
 > Heather
 > ___________________________________________________________________
 >                    Dr. Heather A. Carlson, Ph.D.
 >             American Cancer Society Postdoctoral Fellow
 >       La Jolla Interfaces in Science - BWF Postdoctoral Fellow
 >
 > UCSD, Dept. of Chemistry and Biochemistry     Phone: (858) 822-1469
 > 9500 Gilman Drive, 4202 Urey Hall               Fax: (858) 534-7042
 > La Jolla, CA 92093-0365         E-mail: hcarlson : at : chemcca10.ucsd.edu
 > ___________________________________________________________________
 >
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 --
 --------------------------------------------------------------
 Anil C. Nair                     |
 Computational Chemistry Group    | Phone  :(314)-516-6882
 Department of Chemistry          |
 University of Missouri-St. Louis | Fax    :(314)-516-5342
 8001 Natural Bridge Rd.          |
 St. Louis, MO 63121-4499, USA.   | e-mail :anil : at : ozone.umsl.edu
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