[Zinc-fans] (no subject)

John Irwin jji at cgl.ucsf.edu
Thu Aug 25 15:49:55 PDT 2005


Hi Oshik

SDF is a widely used format created by MDL. Most supplier catalogs come in
(2D) SD format, for example. ZINC SDF are 3D. SDF may contain tagged data
fields in addition to the coordinates. SMILES is a linear notation created
by Daylight. It only implies 3D structure. Both SMILES and SDF are widely
used and supported in the computational drug design field, as is mol2.
Flexibase is a format created by Dave Lorber and Brian Shoichet in this lab
for virtual screening. It is only ready by our program, DOCK3.5.54, so far,
although there are plans afoot to have other programs read it.

Hope this helps.

John

> -----Original Message-----
> From: zinc-fans-bounces at docking.org 
> [mailto:zinc-fans-bounces at docking.org] On Behalf Of 
> oshikseg at post.tau.ac.il
> Sent: Thursday, August 25, 2005 12:44 AM
> To: zinc-fans at docking.org
> Subject: [Zinc-fans] (no subject)
> 
> 
> Hello zinc-fans!
> I am new to zinc database. I am trying to run some of the 
> molecule from zinc by
> DOCK5 program. I am able to run the .mol2 files but I dont 
> know how to use the other formats, what are the other format 
> & how can I read them?
> Thank you in advance
> Oshik Segev.
> 
> 
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