On Fri, May 8, 2009 at 11:10 PM, Danni Harris da= nni]![simbiosys.ca &l= t;owner-chemistry+/-ccl.net>= ; wrote:

Sent to CCL by: "Danni = Harris" [danni(!)si= mbiosys.ca]
All the packages mentioned in this thread to date are first rate---and Ihave used most of them to good effect.

Each of these are worth exam= ining in trials ---and if you can afford it
having more than 1-package i= s a good idea. Each has their strengths.

You also want to go read a few reviews on scoring functions---there hav= e
been numerous over the past few years---I'll just mention the late= st one
I've seen:

Cheng, T. Yan X-L., Liu Z., Wang R. =A0&quo= t;Comparative Assessment of Scoring
Functions on a Diverse Test Set." JCIM 49:1079-1093 (2009).

You= may also want to download and try eHiTS. It is available for 1-month
de= mo's---and low cost.

Two of the aspects I see as strengths for t= his own package in my own
personal research is a knowledge based scoring function that often giveslow-RMSD/score correlations/separations--such that your top-ranked posestend to be the ones observed in structural biology. I would like to have<= br> some assurance when examining docking paradigms that my Top-Rank poses are<= br>the relevant ones.

One can also 'family' train your own c= ustomized scoring function to
improve this latter facet (if need be) for= particular pharmacological
families.

Here's some blog items to say a few words about these = concepts.
http://www.sim= biosys.ca/blog/2009/05/04/fragment-based-pose-prediction-and-affinity-scori= ng/
http://www.simbiosys.ca/bl= og/2009/03/10/fragment-pose-prediction-and-score-rmsd-correlations/

One last facet---besides running on Intel platforms---you can also set = up
a PS3 'farm' for low cost supercomputing performance. I am cu= rrently doing
this myself for high throughput metabolism predictions. So= for $400.00 =A0I
have a platform that will replace 8-30 nodes on a cluster---and running
= the PS3's in parallel gives nearly linear scaling.

Danni

=
>
> Sent to CCL by: "neeraj =A0misra" [neerajmisra[-= ]hotmail.com]
> PLEASE SUGGEST SOME GOOD PACKAGE FOR DOCKING STUDIES AND MD SIMULATION= .>
>

--
Danni Harris, Ph.D.
Scientific Sales and = Support Executive
Computational Chemistry Software Development
SimBio= Sys
135 Queens Plate Dr.; Unit 520
Toronto, Ontario
M9W V61, Canada
Te= l. Head-Office: 416-741-4263
Mobile: 650-799-6637
Fax: 416-741-5084Web: http://www.si= mbiosys.ca

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