docking.org

Dear DOCK Blaster Users

Some of you have had problems with continual email notifications, caused by our system getting stuck. We have turned email notifications off until we can review this problem. We apologize for the inconvenience.

John

Dear ZINC Users

Today we deleted 11,231 corrupted molecules in ZINC. The complete list is here http://zinc.docking.org/broken/January-6-2010.smi.txt. Each line contains the corrupted SMILES followed by the ZINC ID. We might have been able to fix some of these, but we worried about not correctly capturing the correct original molecule. We therefore decided to delete, and to reload the molecules from the original source catalog.

We also "retired" 79 molecules that were duplicated. Thus the "old" ZINC ID now redirects to the new ZINC ID when you use the ZINC search tool.

Dear docking.org users

We will be doing a little open heart surgery on our website (ZINC, DOCK Blaster, etc) over the next 24 hrs - Tues Jan 5 pm to Wed Jan 6 am. We will try to keep the disruption to a minimum, but we are pretty sure that things will break. When they do, we'll try to put them right as soon as we can.

This reorganization is to allow us to develop new services.

John

We changed over some software this afternoon, and some services probably did not work during a 45 minute period. If you were using docking.org services today 12:45-13:30 San Francisco time, we regret the inconvenience. Please just re-do whatever it was you were doing. It should work now.

-- John

Dear docking.org Fans

We thank you for your interest and support over the past year, and look forward to helping you find new chemistry for your biological targets in 2010!

As always, we welcome your questions and comments, and will do our best to help when we can. Due to our limited resources, we are often not able to respond immediately, but we will try to get back to you as soon as we can.

-- John

Dear DOCK Blaster Users

Due to an administrative error, jobs ending in 7 that were submitted in the last 2 days (Mon 14 Dec) failed. If this is you, please resubmit your job.

Due to another administrative error, jobs ending in 0 submitted between Dec 1st and Dec 13th (2 days ago) have been lost. Again, please re-submit your job if you are affected.

We regret these errors and will try to be more careful in the future.

-- John

Dear ZINC Users

We are transitioning to a new incremental subset system, with the aim of providing a more useful service. Here is the background.

Often, people screen either "leads" or "fragments" as the first docking run. They then wish to move to a larger subset, like "drug like" (#3), "all purchasable" (#6), "lugs" (#78) or "flagments" (#77). The first three of these also contain the leads, while the last of these contains all the fragments. It seems a shame to have to rescreen 3.2 M (or whatever) that have already been screened.

Our news for the day are:

1. New subset #11
2. Updated 60,70,80,90 Tanimoto representatives for #6, "all purchasable" and #13, "clean drugs"

John

Dear docking.org users: Here is a round up of recent news:

1. New subset 11 (lead-like) 3.4 M compounds that we believe you can purchase.

2. We are finishing up updating ZINC. Actually, it is a never-ending process. Still, we are in the process of re-generating many of the most commonly used subsets. (See #1 above)

3. There is a new version of Chimera available. We have checked, and DOCK Blaster is compatible with the new Chimera on Linux (Fedora), Mac 10.5 (probably .4 and .6 too) and Windows XP.

Sorry, some people are misusing this site. I have locked it down. If you want to post, contact me. I hope this lockdown will stop this SPAM. Sorry you had to see it.

-- John