We help you discover chemistry for your biological targets.

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

docking.org will be down next weekend

Dear docking.org users, including DOCK, ZINC, DUD, HEI, SEA, DOCK Blaster among others:

Our server will be down next weekend. (Oct 30 - Nov 1). This starts 4 days from now (Fri Oct 30, 5pm local time) and lasts for 2-3 days. The purpose is to install new equipment and perform some deferred maintenance.

The system will be up by Monday Nov 2, and will probably become ready sometime on Sunday Nov 1.

Please plan accordingly.

-- John

Fall ZINC update in progress

Dear ZINC Users

A major update of ZINC is in progress. As of today, we have updated the catalogs for:

- Maybridge
- Maybridge Building Blocks
- InterBioScreen Building Blocks
- MP-Bio
- BioBlocks
- Vitas-M Building Blocks

The following updates are currently in progress:

- Enamine
- Enamine Building Blocks
- Aurora
- Aurora Building Blocks
- AmbInter
- Otava
- Otava Tangible

Molecule upload was broken this weekend (Sept 25-28). Fixed.

New rule: never make changes to code just before you leave on Friday.

I broke molecule upload on Friday about 5:30pm local time. It was put right Monday at 1.30pm local time. Between those two times, molecule upload will probably not have worked. In addition, various DOCK Blaster features that depend on molecule upload may not have worked.

The workaround is to simply re-submit the job / re-upload the molecule.

We regret the inconvenience this has caused.


DOCK Blaster bug fix - multiple docking runs

Attention DOCK Blaster users:

We fixed a bug this morning that had been causing quite a bit of confusion. The bug was: when you dock a second database, it would disappear from the interface. So some people were docking again and again, each of which would go away.

The was a pure book keeping problem, but it was really annoying for some people. We have tested it, and it seems to work, as of this morning.

Please let us know if you are still having difficulty with this bug, which we are calling the "second and later docking screens disappear" bug.

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