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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.

Changes in default sampling, effective Sept 10, 2009

Dear DOCK Blaster users,

We made changes in the sampling schemes ("coarser", "finer") used by DOCK Blaster effective Sept 10, 2009. We expect jobs should run much as they did before the change, but we are performing a thorough study to check our prediction.

-- John

Metalloenzyme issues in DOCK Blaster, Aug 28 - Sept 11, 2009

Dear DOCK Blaster Users:

We discovered a problem that may have produced strange results for any DOCK Blaster job containing a metalloenzyme - often Zn - coordinated by one or more histidines. This problem was in effect between Aug 28 and Sept 11, 2009 at 4:30pm.

If you started a DOCK Blaster job in that time frame, please discard the previous results and run your new job.

-- John

Arylamines: A new front on the war on error

Dear patient ZINC users:

You may have been as puzzled as we were by the nearly 100,000 protonated arylamines in the physiological pH range (6-8) in ZINC as of August 2009. Now whereas the pKa of amines on aryl rings does vary rather over a couple of logs based on the subsitution pattern both on N and the ring itself, it is a good rule of thumb that these compounds are rarely protonated, unless the pH is say 5 or lower.

Minor clean up - Sept 8th, 2009

We have been doing some housekeeping, listed below. When changes are made in ZINC, exported subsets will only be corrected if they were exported after Sept 8, 2009.

= ZINC =
1. We found and fixed 64 ZINC entries with incorrect protonation of triaminopyrimidines.

2. We found 112 ZINC entries with incorrectly protonated arylhydrazines: [NH3+][NH]a. We deleted these completely from ZINC, and have reloaded them, so they now have new ZINC IDs. We regret this, but it was the only practical way.

The DOCK Blaster paper has appeared

"Automated docking screens: a feasibility study" has appeared at J Med Chem, ASAP.

Here is the link: http://pubs.acs.org/doi/abs/10.1021/jm9006966

We hope you find it interesting and look forward to discussing with you.

-- John

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