From jji at cgl.ucsf.edu  Thu Dec  6 14:35:39 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 06 Dec 2007 14:35:39 -0800
Subject: [Zinc-fans] Comparison mol2 and smiles files
In-Reply-To: <474A8857.9030909@chemiome.chm.unipg.it>
References: <474A8857.9030909@chemiome.chm.unipg.it>
Message-ID: <4758793B.2090204@cgl.ucsf.edu>

Hi Emanuele

I am finally getting back to your question. You are quite correct. I
just did:


>  zmore sial_p0.smi.gz | awk '{print $2}' | sort -u > smiles_codes  
>  zcat sial_p0.?.mol2.gz | grep ZINC | sort -u > mol2_p0_codes
>  wc -l smiles_codes mol2_p0_codes
 114763 smiles_codes
 112069 mol2_p0_codes
> diff smiles_codes  mol2_p0_codes  |wc -l
4265

I agree that there are a little over 2,500 differences in the mol2 and
SMILES of Sigma Aldrich in ZINC version 7, a little over 2% of the
library. This is of course wrong, and we will attempt to do better in
future versions.

Thank you for reporting this. I have put it on the ZINC errata page,
which I am finally getting around to updating.
http://wiki.compbio.ucsf.edu/wiki/index.php/ZINC:Errata

John



emanuele wrote:
> Dear all ZINC-fans,
>
> I downloaded the databases Asinex and Sigma-aldrich from the version 7 
> of ZINC in both the formats SMILES and MOL2.  For both the databases I 
> found a difference in the molecules present in the archives, that means 
> some molecules present in the multi-mol2 file and not in the SMILES and 
> vice versa.
>
> Is it possible or I did some errors in the comparison?
>
> Thanks in advance
> Regards,
>
> Emanuele
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>   

From psivapra at olemiss.edu  Thu Dec 20 07:29:14 2007
From: psivapra at olemiss.edu (Sivaprakasam Prasanna)
Date: Thu, 20 Dec 2007 09:29:14 -0600
Subject: [Zinc-fans] zinc in catalyst format
Message-ID: <476A8A4A.5010503@olemiss.edu>

Hi all,
I am wondering about any ways I can get Zinc subsets in catalyst 
software database format to do virtual screening. Right now I cant 
convert Zinc .sdf database to catalyst .bdb format.
Any help?
Prasanna


From jji at cgl.ucsf.edu  Thu Dec 20 10:42:54 2007
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Thu, 20 Dec 2007 10:42:54 -0800
Subject: [Zinc-fans] zinc in catalyst format
In-Reply-To: <476A8A4A.5010503@olemiss.edu>
References: <476A8A4A.5010503@olemiss.edu>
Message-ID: <476AB7AE.90704@cgl.ucsf.edu>

Hi Prasanna

Catalyst should offer a tool to convert .sdf to .bdb.

>From google "convert sdf catalyst bdb":

Here's a reference to a guy who can do it (but he has other problems)
http://server.ccl.net/chemistry/resources/messages/2006/11/15.008-dir/index.html

>From google "catalyst bdb"
Here's a reference that clearly implie that it is possible with the
"CatDB" tool.
http://www.accelrys.com/reference/cases/studies/fliptutorial.pdf

Good luck!

John

Sivaprakasam Prasanna wrote:
> Hi all,
> I am wondering about any ways I can get Zinc subsets in catalyst 
> software database format to do virtual screening. Right now I cant 
> convert Zinc .sdf database to catalyst .bdb format.
> Any help?
> Prasanna
>
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>