Subject: Generating conformations

From: Markku Laukkanen <[email-masked]>
Date: Wed, 19 Feb 2003 07:08:11 +0200 (EET)

Hi!

Is there any known free or low cost program generate low energy
conformations for given molecule to use in docking experiments?

Any help is appreciated!

Thx,
	PKY

---

From: Szilveszter Juhos <[email-masked]>
Date: Wed, 19 Feb 2003 10:19:00 +0000 (GMT)

> conformations for given molecule to use in docking experiments?

Try:

GOLD:      http://www.ccdc.cam.ac.uk/prods/gold/
FlexX:     http://cartan.gmd.de/flexx/
AutoDock:  http://www.scripps.edu/pub/olson-web/doc/autodock/index.html
Glide:     http://www.schrodinger.com/Products/glide.html (once their web 
           server is back)

Most of them have a demo version (or you can ask for). If you want to make
more elaborate docking experiments, that is a problem :-/ For AI/data
mining likely you need quite a few poses and a good knowledge of the
target.

Hope it helps:
Szilva

---

From: Markku Laukkanen <[email-masked]>
Date: Wed, 19 Feb 2003 12:45:51 +0200 (EET)

> mining likely you need quite a few poses and a good knowledge of the

The problem is, that we have our own GA docking module, which is quite
accurate and fast docking rigid/rigid pairs to known (5 -20 å radius)
binding pocket. So I am not necessarely interested in evaluating one of
those :-)

But I would like to get a piece of software, where I could e.g. ask for
10000 least energy conformations (e.q. with certain energy margin as a 
difference) & dock those after that using GA & marginally flexible
conformation instead.

When I try to used totally flexible ligand and more than 20 rotors, it
quite often happens, that the amount of conformations using torsion
library to analyze the possible torsion angles for conformations exceed
the limit of 32 bit integer :-) And the time to do the docking exceed the
time for me to wait next to computer.

I downloaded tinker and tried it ( thanks to Per-Ola Norrby
<[email-masked]> ) , looks quite promising but
would require more information how to use it. Also I would like to
integrate everything with my c++ code piece.

PKY