John Irwin's blog

downtime today

Dear 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 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 users

We are having trouble with the decoy generator, and thus 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.,

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.


Dear 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 back up

Dear fans

About 90% of 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

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