Simple docking

Yoram Puius puius at aecom.yu.edu
Sat Aug 1 14:24:28 EST 1998

Hi all,

Basic modeling question:  I have a theoretical model of two docked
molecules, and its godawful.  However, I think that the basic binding
mode is okay, so I'd like to just do some simple refinement and see if

1) I can relieve the bad contacts
2) I can get some degree of surface complementarity in the process

What would be the easiest way of going about this?  How hard would
it be to do a rigid-body refinement in X-PLOR with the xray term
off, but with vdW and electrostatics on, and how well does that
work in people's experience?  Do you get the molecules flying apart
due to a couple of bad contacts?

Alternatively, is there a better program to use?


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
"Naturally I have other work here, crystal structure, but often I
wonder which is more useful, silly hobby or vital science."
				- Don DeLillo, "Ratner's Star"

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