Ivan Torshin wrote:
>> Hello, everyone,
>> Could you help me: how to locate active site chain segments,
> having only structure of native enzyme ?
> Question is rather "general", any ideas, references ?
>> Thank you beforehand,
> Ivan.
Try computational functional group mapping, i.e. finding places on
the surface where small groups that look like the substrate (e.g.
phosphates, formates) can be docked. A program frequently used for
this is called MCSS. Check out the following references:
An automated method for dynamic ligand design.
Miranker A. Karplus M.
Proteins. 23(4):472-90, 1995 Dec.
Multiple copy simultaneous search and construction of ligands in binding
sites: application to inhibitors of HIV-1 aspartic proteinase.
Caflisch A. Miranker A. Karplus M.
Journal of Medicinal Chemistry. 36(15):2142-67, 1993 Jul 23.
Comparison of experimental and computational functional group mapping of
an RNase A structure: implications for computer-aided drug design.
Joseph-McCarthy D. Fedorov AA. Almo SC.
Protein Engineering. 9(9):773-80, 1996 Sep.
Functionality maps of binding sites: a multiple copy simultaneous search
method.
Miranker A. Karplus M.
Proteins. 11(1):29-34, 1991.
Enjoy,
Y
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Yoram A. Puius Albert Einstein College of Medicine
6th year M.D.-Ph.D. Department of Biochemistry
mailto:puius at aecom.yu.edu 1300 Morris Park Avenue, Bronx, NY 10461
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