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ZINC applications

Dear ZINC fans

We like to share and have shared with us successful research studies, and it is particularly nice if they use our software and databases. You may therefore be interested in "Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays." by Colizzi (yes, THAT Colizzi, co-author of the DOCK Blaster 2009 paper), that just came out in Method Mol Bio. http://www.ncbi.nlm.nih.gov/pubmed/24318892, http://link.springer.com/protocol/10.1007%2F978-1-62703-730-3_11.

ZINC

Hello friends,
I couldn't able to download the SDF file from ZINC. they are only giving .csf file. what to do? suggest me?

Discovery of JQ1

This is a new era for the scientists those are looking forward to develop a prototype compound for various life threatening diseases like cancer, HIV, etc. The open source funding or else we can say the kits are useful for dextop drug designing. JQ1 was discovered by Jay Bradner really a remarkable achievement in Cancer field. We are looking forward for more exciting tools in open source arena.

How do I list my catalog in ZINC?

Dear Vendors

If you want your catalog to be listed in ZINC, please send your catalog in SDF format to John Irwin by email (jir322 at gmail dot com). If your catalog is too big to put in email, send us a URL where we can download the catalog. We will acknowledge receipt and get you set up promptly.

If you have a catalog update, please send those along when you have them. We like to receive complete catalogs so that we can verify compounds from the previous catalog are still for sale, or, if not, mark them as depleted in ZINC. We aim to update at least quarterly.

2014

Dear docking.org fans

We made a typo on Jan 3 that led to the DUDE decoy generator (and by extension DOCK Blaster that depends on it) not working for 4 days. Normal service was restored yesterday Monday Jan 6 around 6pm San Francisco time.

Things should be working normally now. Let me know if that is not true.

We regret any inconvenience.

I also "cleaned up" a bunch of old docking jobs that were in an unusable state. I tried to be careful, but if I accidentally wiped out your job that you still wanted, I regret that. Please resubmit and accept my apologies.

John

docking.org back up

Dear docking.org fans

About 90% of docking.org services have been up since about 8am this morning in San Francisco. A couple of things are still giving us trouble. We are working on them, and expect everything to be normal again by Friday morning.

-- John

14 hour power out tonight - docking.org offline

Dear docking.org fans

Due to an interruption of electrical power beyond our control, our sites ZINC, DOCK Blaster, SEA, DUD, DUDE, and so on will be down overnight for a planned power outage.

San Francisco time, the outage will start at 4 to 6 pm and last until 8 am Thursday morning. This will be the longest planned outage any of us can remember.

This is related to the new hospital across the street, which will be opening soon. If you find yourself in San Francisco, check out Mission Bay. If you've been there before but not recently, you won't recognize the place!

Something to be thankful for - DOCK Blaster is back to normal

Dear Patient Users

Wednesday evening DOCK Blaster was restored to normal pre-attack (Nov 11) level service. Interestingly, the scoring #2 "AMBER scoring" had been working, but the Scoring #1 "polarized binding site" aka "tarted up" scoring had been incorrect, due to a typo. Weird! We regret the trouble, and will do our best to:

a. keep the service running smoothly as best we can

b. write to all of you who have written me with follow up explanations and assistance.

Please give me 2 days to catch up on my email backlog.

Happy Thanksgiving!

John

DOCK Blaster mechanically working

Dear users

DOCK Blaster started working mechanically again Friday afternoon around 2pm San Francisco time / 5pm Toronto time. However, although the program runs to completion, there does seems to be a parameterization problem that is causing too many small anions to score well (at least in one case I tried).

Therefore, please be careful. I am continuing to test DOCK Blaster and investigate this problem, and will let you know as soon as I know what is wrong.

John

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