docking.org

We currently maintain four ZINC versions: ZINC 5, 6, 7, and 8, released in 2005, 2006, 2007 and 2008 respectively. Generally, ZINC grows each year as we add more compounds, and more suppliers. But it also shrinks as compound stocks become depleted.

We recommend the use of ZINC 8 for all purposes. The only reason we can think of for using old ZINC versions is to access molecules that may have vanished for one reason or another in the latest version.

In particular, the search feature, upload feature, and subset features are best in or only are available for ZINC 8.

Starting today, searches in ZINC 8 will search over 10M compounds. Previously, substructure searches only searched about 2.5 M compounds in ZINC, because we were not updating our search dictionary.

Thus, if you previously did not find what you were looking for, look again, it may be there!

Please note that searching quotas are in effect, to allow us to offer this service for free to everyone.

This is one more step in the slow-but-coming ZINC 8 release.

All docking.org services are back on line. If you used docking.org over the past 24 hours and had a problem, please try again.

A group at IBM in collaboration with Terry Lang have published a "RedPpaer" through the IBM website:

High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System

The "Multiconf-DOCK" package of Miteva and Villoutreix is now available from the DOCK website

http://dock.compbio.ucsf.edu/Contributed_Code/index.htm

This work will appear in BMC Bioinformatics shortly:

Sauton N., D. Lagorce, B.O. Villoutreix, M.A. Miteva. MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMCBioinformatics, 2008, 9:184

We thank Miteva and Villoutreix for contributing their code!

We are doing maintenance on our cluster this Friday and Saturday. docking.org services may be down starting Friday around 5pm through all day Saturday, local time. Sorry for any inconvenience.

We are being clobbered by search and subset requests in ZINC this morning. We have had to cancel all jobs and restart the server a couple of times, which we regret doing.

On the one hand, this is good news, since people are using ZINC!

On the other hand, we need to change how we do things to provide more robust service. We are doing that this morning.

We updated some software on Thursday that broke DOCK Blaster for about a day and a half. If you submitted a new job during that time, simply run it again please.

The molecule upload-and-process feature of ZINC 8 had an error and must not have been working correctly for a couple of weeks now. It has now been fixed, and seems to be working correctly. We now display helpful messages about the content of files at the bottom of the page where you can download processed molecules that have been uploaded.

File upload from all previous ZINC versions (5,6,7) all point correctly now to ZINC 8 .

Subset create (accessed from the search results page) has been broken for a long time. It is being fixed today.

I have not been using our automatic incident ticket system ("OTRS") correctly. If you have sent email to support at docking.org, my reply may not have been (probably was not) forwarded to you. I regret this error. It should not happen again going forward.