We help you discover chemistry for your biological targets.

New Fragment-like and lead-like subsets of ZINC

New Fragment-like (#2) and lead-like (#1) subsets of ZINC were released yesterday (Nov 3, 2009). These subsets are updated to include over 200,000 depletions (compound no longer for sale) and over 300,000 new compounds (newly on the market).

We are midway though our fall update. These subsets will be updated again before the end of 2009. Updates to other subsets and catalogs are in progress and will be announced as they become available.

-- John

Why Use DOCK?

Sometimes people ask us why we think they should use DOCK and not some other docking program. Of course, we openly admit our bias. DOCK is the program we develop and the one we know best. But that is not all. We have put together a short presentation of why we think you should consider using DOCK for your next ligand discovery project.


-- John

Predicting new molecular targets for known drugs

Our Nature paper has appeared. Please check it out!

We are back

docking.org is back up. Many, many little changes were made, so there is a good chance some things will not work. If you notice something that used to work that no longer works, please write me directly jji at cgl dot ucsf dot edu and I will try to fix it asap.

5 more hours until docking.org goes off line

docking dot org is going off line
the hour is getting late
in just five hours it will be time
for your jobs to terminate

Neither goblins nor witches
but harddisks and switches
is where we focus our attention
this Hallowe'en

in just two days, maybe three
our servers should be up
now get back to work John

ZINC available in Autodock (pdbqt) format

ZINC molecules formatted for Autodock are now available at http://zinc.docking.org/pdbqt/.

Like all of ZINC, these files are free for everyone to download from our site, but you may not redistribute them without written permission from John Irwin.

The files are available as tarballs or as individual files. This work was done to support the FightAIDS@Home project. The availability of this resource is being advertized in Volume 8 of the FightAIDS@Home newsletter: http://fightaidsathome.scripps.edu/

The files were prepared by Stefano Forli and communicated

docking.org down tomorrow - Friday afternoon - for 2 days

Remember that docking.org, ZINC, SEA, and everything else goes off tomorrow, Fri Oct 30 at 5pm for 2 days while we upgrade hardware. Any job running at 5pm will be summarily killed. System will be back up on Monday Nov 2, possibly sooner.

-- John

ZINC fall update - Part 3

We have updated:

- IS Pharm
- IS Pharm Building Blocks
- IS Pharm Make-on-Demand
- Enamine Building Blocks

We are working on new versions of
- drug like (#3)
- lead like (#1)
- fragment like (#2)

These will appear soon. After that, more catalogs will be updated.

ZINC fall update - Part 2

The following catalogs have just been updated:
- Vitas-M
- Otava Building Blocks
- Otava Tangible

Special-purpose subsets updated: 79 and 80

More catalog updates and subset exports are in progress. We will try to report once a week for the next month on our progress. The entire process should be complete by the end of Nov. 2009.

-- John

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