We help you discover chemistry for your biological targets.

ZINC and the rest of docking.org is back up

We were down over the long weekend, beginning Sunday morning through early Monday morning in San Francisco. We are back up now. Thank you for your patience.

download (large) arbitrary subsets based on ZINC ID

People ask "how can i download 100,000 (or more) custom ZINC molecules in say mol2 or SDF format" . Well, there's an old saying that goes, give a person a custom database and they'll dock for a day. Give them a wiki page that describes how to download arbitrary and arbitrarily large subsets in a format of their choosing and they'll dock for a lifetime. In that spirit, I give you http://wiki.uoft.bkslab.org/index.php/ZINC_via_curl you give the script a list of ZINC IDs as test.list. We split them up into chunks of 1000, and download each molecule separately.

docking.org is up and running

We're just happy to tell you that we have not been down now for a whole day, and things seem to be working much better. Be sure to let us know if you have any trouble at all!

-- John

downtime today

Dear docking.org fans

We are back up (8:30am in San Francisco) after at least 6 hours offline. A disk server had crashed, and our remote control scripts did not work.

Sorry for any inconvenience and thank you for your patience.

-- John

hardware troubles in San Francisco

some services are backed up and appear not to be working. In fact, the queue is just very long until we repair a disk. Sorry for the trouble, and thank you for your patience.

fgfr1.tar.gz fixed on DUDE website

Dear DUDEs

I finally fixed fgfr1.tar.gz on the DUDE website. So sorry for this typo that led to the decoys in mol2 and SDF format for this target not being included in the distribution.

-- John

dude.docking.org/generate back up - try your failed requests again

Dear Decoy fans

Our decoy maker got overloaded on Feb 28, and, after being politely nagged by people since then, we finally got around to resetting the machine today.

Decoys should now work again, as should DOCK Blaster which depends on making decoys.

If you submitted a request to our server that did not complete since Feb 27, we recommend you resubmit it. That is going to be by far the fastest way.

having trouble with the decoy maker

Dear docking.org users

We are having trouble with the decoy generator, and thus dude.docking.org/generate and DOCK Blaster are both currently getting stuck. Please be patient and we will try to have this resolved by tomorrow.

-- John

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.

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