Internal: migration to new MySQL servers complete

Today (Oct 15 2007) from 10am-2pm, we migrated from our old mysql server #148 to the new ones at zincdb1/2. During the transition period, and until 3pm, some services may have ended abnormally and/or produced unexpected results. The workaround is to just re-run anything you ran during that time that you suspect may not be right.

As of 4pm local time, we believe ZINC, DOCK Blaster, and other services are working correctly. If you notice any strange behavior, please report to support at

xmlrpc services at (including DOCK Blaster) will be down 4pm-6pm Thu Sept 6 2007 SF time

We are upgrading the XMLRPC support at Various features may be unavailable and/or may fail mysteriously during this time. Normal service will be restored by 5.30 pm. All problem reports after that time to support at please.

XML RPC services are back up (4.32 pm SF time). Further details in the attached comment.

Meeting Announcement: MedChem USA - 10 & 11 Oct '07

John Irwin will be speaking at the MedChem USA 2007 meeting in Boston, October 10th 2007. I'll be talking about DUD, ZINC, and how to make docking easier to use and more reliable, especially for non-specialists.

Here's the URL

Andrew Good's raw DUD data from ACS now available

Andrew Good has kindly made available the data he discussed at the ACS in Boston last week (Aug 21, 2007). We have posted it on the DUD website in two categories: DUD Clusters and Wombat data. Each posting has a write up "summary.{doc|pdf}" that describes how the data were prepared.

This posting may be of interest to anyone who is benchmarking 3D virtual screening methods.

The data will be curated, and may be incorporated into a future version of DUD. For now, they are available as raw files.

current status of websites @

The following websites are currently public and supported here at

* ZINC7 - the 2007 version of ZINC. (
* ZINC6 - the 2006 version of ZINC. (
* ZINC5 - the 2005 version of ZINC. (

Generally, you should use the latest version. However, for maximum backwards compatibility and support of the community, the old versions are still available. A major update is in progress and will be announced soon.

* DUD - A directory of useful decoys for benchmarking molecular docking. has moved to a new server has moved to a new server. We have started using drupal to run our blog, which we hope you will find easier to use.

ZINC, DUD, and DOCK Blaster have also been moved to the new server. We've checked and double checked, but there still may be some problems. So if you see anything that doesn't work (that used to work!) then please let us know.

Thank you for your continued support of our work here at We look forward to helping you discover new chemistry for your biological projects.

new blog

This is my first blog entry for the new blog. We have changed from slash to drupal to enable more flexible and powerful use of the site. Please let us know what you think about our new look.


Testing drupal

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