Subject: CCL:Any good paper on Grid-based interactions?

From: "Carsten Detering" <[email-masked]>
Date: Fri, 29 Mar 2002 18:48:40 +0100

>
>Hello,
>I wonder if you can tell me some good articles on the methods of
>grid-based potential calculations. The more detail and more updated, the
better.

Essentially, there are three ways of calculating grid-based potentials out
there:
the first is used in AutoDocks AutoGrid
Morris, G. M., D. S. Goodsell, et al. (1996). "Distributed automated docking
of flexible ligands to proteins: Parallel applications of AutoDock 2.4." J.
Comp. Aid. Mol. Des. 10: 293-304,
Morris, G. M., D. S. Goodsell, et al. (1998). "Automated Docking Using a
Lamarckian Genetic Algorithm and an Empirical Binding Free Energy
Funcition." J. Comp. Chem. 19(14): 1639-1662., SCF described in:
Mehler, E. L. and T. Solmajer (1991). "Electrostatic effects in proteins:
comparison of dielectric and charges models." Protein Engineering 4(8):
903-910.original grid method described by Goodford
Goodford, P. J. (1985). "A Computational Procedure for Determining
Energetically Favorable Binding Sites on Biologically Important
Macromolecules." J. Med. Chem. 28: 849-857.

There are programs like MEAD
Bashford, D. and K. Gerwert (1992). "Electrostatic Calculations of the pKa
Values of Ionizable Groups in Bacteriorhodopsin." J. Mol. Biol. 224:
473-486.
Bashford, D. and M. Karplus (1990). Biochemistry 29: 10219-10225.
or like DELPHI (MSI)
Honig, B. and A. Nicholls (1995). "Classical Electrostatics in Biology and
Chemistry." Science 268: 1144-1149.
which calculate electrostatics by solving the PB equation. The above
mentioned three ways are especially useful for calculating the electrostatic
interaction in solution.
The new release of DOCK5 (Kuntz et. al., UCSF) will use a Generalized-Born
approach.

Hope this helps you.

Carsten

------------------------

Carsten Detering,Ph.D
University of Washington
Seattle, WA 98195
Phone: 206 543 5081
email: [email-masked]