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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.

http://www.nature.com/nchembio/journal/v5/n8/abs/nchembio0809-536.html

The Wetzel paper on Scaffold Hunter is here:

http://www.nature.com/nchembio/journal/v5/n8/abs/nchembio.187.html

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.

Have you ever had trouble with docking?

Have you run a docking campaign, including purchasing compounds and testing them, only to find that nothing worked? What do you think went wrong? Do you think you could have done better if you had done things differently, or do you believe the project was doomed from the start?

I am interested in hearing from you. You can reply to this blog post, or you can write to me privately at jji at cgl dot ucsf dot edu. It does not have to be long. I am looking for stories of failure, with the aim of learning how to make docking better.

I hope to hear from you!

-- John

To get compound from NPD' "Not for Sale"'

Hi ,

I am using the NPD for virtualscreening. I would like to purchase one of the compound from that database, but unfortunately the purchase info of that compound shows "Not for Sale". Can you pleas tell me how can I get that compound?

The Zinc ID is ZINC13393245

Waiting for reply,

thanks,
Aswathy
Amrita School of Biotechnology
India

Old ZINC versions being retired

We are retiring the old versions of ZINC.

Versions 7, 6 and 5 are now all over two years old. Given the huge turnover in the chemical marketplace, we can think of no reason why anyone would want access to such old versions of the database.

Still, if you do need access to old versions of ZINC, please write us and we will do our best to help you.

-- John

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