John Irwin's blog

Clobbered by search requests this morning

We are being clobbered by search and subset requests in ZINC this morning. We have had to cancel all jobs and restart the server a couple of times, which we regret doing.

On the one hand, this is good news, since people are using ZINC!

On the other hand, we need to change how we do things to provide more robust service. We are doing that this morning.

DOCK Blaster was down Thu Apr 17 10am - Fri Apr 18 9pm. Fixed.

We updated some software on Thursday that broke DOCK Blaster for about a day and a half. If you submitted a new job during that time, simply run it again please.

upload in zinc8 was not working - fixed

The molecule upload-and-process feature of ZINC 8 had an error and must not have been working correctly for a couple of weeks now. It has now been fixed, and seems to be working correctly. We now display helpful messages about the content of files at the bottom of the page where you can download processed molecules that have been uploaded.

File upload from all previous ZINC versions (5,6,7) all point correctly now to ZINC 8 .

Subset create (accessed from the search results page) has been broken for a long time. It is being fixed today.

support at docking dot org email

I have not been using our automatic incident ticket system ("OTRS") correctly. If you have sent email to support at, my reply may not have been (probably was not) forwarded to you. I regret this error. It should not happen again going forward.

ZINC8 export in progress

We are in the "final throes" of the preparation of the new ZINC release. We will try our best not to break anything. Should you notice anything that used to work stop working, please a) wait 24 hrs for me notice it myself, b) write us at support at where I will try to fix it asap. Thank you for your patience and your support.

ZINC search using SMILES/SMARTS was failing Dec 12 & 13

We have recently done some housecleaning that appears to have reduced or eliminated the failures that a lot of people were seeing when searching ZINC. Thank you for your patience and your support.

protein folding as a game

check out for FoldIt! - a video game version of Rosetta. Addictive. Don't say I didn't warn you.

SAMPL-1 - statistical assessment of the modeling of proteins and ligands

OpenEye are running a docking competition based on experimental data donated from Abbott, Vertex and GSK. for more info and to sign up. Several separate competitions and several separate deadlines, but it'll all be over in Feb'08. There is a meeting mid-March'08 in Santa Fe, a la CASP, to review the "winners". Of course you know we all win from efforts like this. Thank Ant and Geoff for making this happen.

Papers we are reading

There are a few papers that have caught our attention recently, and I thought I would share them with you. This won't be news for many of you who read the journals as they come out.

1. "Virtual exploration of the Chemical Universe...", the second paper, by Fink and Reymond.

This work by Reymond enables us to begin to ask quantitative questions about chemical space, at least at low molecular weight. I think this database can be a very useful, pragmatic way to think about "what are we missing in chemical space?"

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