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Arylamines: A new front on the war on error

Dear patient ZINC users:

You may have been as puzzled as we were by the nearly 100,000 protonated arylamines in the physiological pH range (6-8) in ZINC as of August 2009. Now whereas the pKa of amines on aryl rings does vary rather over a couple of logs based on the subsitution pattern both on N and the ring itself, it is a good rule of thumb that these compounds are rarely protonated, unless the pH is say 5 or lower.

Minor clean up - Sept 8th, 2009

We have been doing some housekeeping, listed below. When changes are made in ZINC, exported subsets will only be corrected if they were exported after Sept 8, 2009.

= ZINC =
1. We found and fixed 64 ZINC entries with incorrect protonation of triaminopyrimidines.

2. We found 112 ZINC entries with incorrectly protonated arylhydrazines: [NH3+][NH]a. We deleted these completely from ZINC, and have reloaded them, so they now have new ZINC IDs. We regret this, but it was the only practical way.

The DOCK Blaster paper has appeared

"Automated docking screens: a feasibility study" has appeared at J Med Chem, ASAP.

Here is the link: http://pubs.acs.org/doi/abs/10.1021/jm9006966

We hope you find it interesting and look forward to discussing with you.

-- John

About 12M ZINC compounds disappeared from PubChem this week. WHAT?

We revoked 12M ZINC compounds from Pubchem this week. We thought you might like to know more about this. If so, read on...

Automated docking party on 9/9/9.

We are holding an automated docking party to celebrate the release of DOCK Blaster on 9/9/9. Free docking for everyone, and some free beer too.

docking.org downtime Friday evening in San Francisco (correct)

docking.org will be rebooted Friday evening circa 5.30pm - 6.30 pm local time.

Everything will stop cold for up to an hour while we upgrade our equipment.
Thank you for your interest, support, and patience.

CSAR: Community Structure Activity Resource

The Community Structure Activity Resource at Michigan University starts its first public challenge tonight at midnight. We've already booked our tickets on the bullet train from Tokyo airport so we can be among the first to savor the "PDB nouveau". There will be a session at the spring ACS in San Francisco in 2010 to discuss this. If you want to participate, you need to submit by Oct 5, so don't just sit there.

Please take a look at their website, http://csardock.org/ and see what you think of it.

Staring off into chemical space

My News and Views about Scaffold Hunter and Scaffold Tree appeared this week in Nature Chemical Biology.


The Wetzel paper on Scaffold Hunter is here:


If you haven't checked out this software yet, take a look. I am particularly happy that they GPL'd the code. http://scaffoldhunter.sourceforge.net/. Congratulations to Stefan and Co. !

new extrema and random databases in DOCK Blaster today

We are making many improvements to DOCK Blaster. Recently, we introduced a new color-coded preliminary docking assessment table that aims to provide a yes/maybe/no answer to the question: Should I continue with docking. We thank the referees of our paper for prompting us to bring this forward.

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