[Dock-fans] create library for virtual screening from ZINC

Sudipto Mukherjee sudmukh at yahoo.com
Thu Jan 12 11:30:09 PST 2012


Dear Dong,

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#DatabaseFilter 

DOCK 6.x includes a database filter which can perform filtering by heavy atoms, rotatable bonds, molecular weight and formal charge on-the-fly. Using the filter, you can make exclusive subsets of a mol2 database during docking (e.g. 0-2,3-5,6-8 rotb, or -1,0,+1 formal charge).
 

Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University



________________________________
 From: John Irwin <jir322 at gmail.com>
To: LIU Changdong <dongyi2827 at yahoo.com.hk> 
Cc: "dock-fans at docking.org" <dock-fans at docking.org> 
Sent: Wednesday, January 11, 2012 1:11 PM
Subject: Re: [Dock-fans] create library for virtual screening from ZINC
 
Dear Dong

Thanks for your question about preparing a library in ZINC.  ZINC
enables you to get large pre-made libraries by properties and vendors,
or small (<5000) libraries by arbitrary criteria. We cannot
(currently) support large arbitrary criteria bigger than 5000, because
of the load it would put on our public server.

If you want libraries selected using arbitrary criteria bigger than
5000 molecules, you have three options:

1. ask me. If it is something that might be popular, we can make it for everyone

2. download a superset in ZINC (e.g. drug-like), and do the selecting
on your local machine

3. realize that one of our pre-made subsets, while not *exactly* what
you want, is close enough for your purposes.


Good docking and good luck!

John

PS.  If you don't log in, you only get 500 molecules.  Use the "next"
button (top left of the listing) to go to the next page.  If you log
in (free registration!) you can get up to 5000 molecules per query.
You only get 100 molecules per page, and you use the next button, or
type the page number you want to jump to.

PPS we are working on allowing arbitrary criteria for subsets of
50,000 molecules available to the general public, which we hope will
be on line before the end of the year.  We are unlikely to support
arbitrary subsets larger than 50,000,  but who knows.

On Wed, Jan 11, 2012 at 12:30 AM, LIU Changdong <dongyi2827 at yahoo.com.hk> wrote:
> Dear DOCK fans,
>
>   I'm just preparing a library for virtual screening from ZINC.
>
>  I'm using the search function on the ZINC website to search the compounds
> which I need, my question is:
>
> 1) after pressing "run query", there's only 1 page( for example 100 for 1
> page), how can I know how many compounds I got based on my criteria.
> 2) How can I download all the compounds which I need, every time I can only
> download   500 compounds in mol2 format.
>
> Thanks in advance for any help!
>
> Best
> Dong
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://mailman.docking.org/mailman/listinfo/dock-fans
>
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