Locating active sites

Yoram Puius puius at aecom.yu.edu
Thu Oct 23 08:42:35 EST 1997

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
Miranker A.  Karplus M.
Proteins.  11(1):29-34, 1991.


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

More information about the Xtal-log mailing list