John Irwin's blog

incorrectly represented diamines

One problem in ZINC has been the representation of di-amine cations, matching the patterns (occurrences) :

[NHv4][NHv4] (2811)
[NHv4]*[NHv4] (7750)
[NHv4]**[NHv4] (268,328)

These molecules are not in a biologically relevant form, due to their improbable if not impossible protonation state. We are now loading these in their biologically relevant protonation states.

ZINC Subset Re-definition

When, in the course of human events, it becomes necessary for us to dissolve the physical property constraints have been used to select screening subsets and to assume among the powers of earth, blah blah blah, subset definitions that make sense, a decent respect to the users of the ZINC website requires that we should declare the causes which impel us to this change.

New policy on old ZINC versions

Until now, we have been making all old ZINC versions available. The purpose was to allow people to look up molecules if they did not download a purchasing spreadsheet when they downloaded the subset (hint: good idea!). This has started to create problems of clarity, and frankly an increasing burden on our systems.

Recent changes - Oct 2008

We are making the final changes in ZINC8, since ZINC9 will take over in January. Here is quick round up:

* Subset re-defintion (think "lead-like", "fragment-like") to better conform to expert opinion in the field. A longer article about this will appear soon

* Subset pruning - we have streamlined the list of available subsets for clarity.

* Depletion - we have depleted over 1M compounds this month. i.e. the compound is no longer available. This will take a while to show up everywhere on our site.

September is fall cleanout month for ZINC

Dear ZINC Fans

A common complaint is that compounds in ZINC cannot be purchased. To try to improve the ratio of compounds you can actually buy, we continually a. load the latest catalogs and b. purge compounds no longer listed in a supplier's catalogs.

During September, we will be retiring catalog entries (and thus possibly compounds) that are no longer for sale, as far as we know. Here is the progress so far. I am using the ZINC short names for brevity. (updated: Sept 5, 2008)

acb, 76; acdisc, 395; acros, 3289; adesis, 19; cdiv 132,000; florida 4; frinton 111; frontier 12;

Summer's almost gone - a progress report

Dear Colleagues:

DOCK Blaster is undergoing some major changes this week and next. Some jobs may be lost, or fail for no obvious reason. We will try to keep the disruption to a minimum. Thanks for your patience.

We continue to load ZINC, about 100K molecules per week, and are approaching the 15 million molecule mark, internally. We foresee 15 million purchasable "drug-like" molecules in current catalogs before the end of 2008.

lookout! here comes

ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services ChemSpider is the richest single source of structure-based chemistry information.

many ZINC and DOCK Blaster services were down Fri Aug 15 11pm - Sat Aug 16 3pm SF time

Many services were down for about 16 hrs last night. Many things will not have been working, due to a critical server being down. If you had any trouble, please try again.

ACS Talks next week

There will be several talks from group members next week. Please come and see us - and stay to chat about docking and ligand discovery.

John Irwin, Quantitatively relating proteins by their ligands,
8:00 AM-11:40 AM, Monday, August 18, 2008 Sofitel -- Versailles, Oral

Brian Shoichet, Druggability and chemical space in fragment docking,
8:00 AM-11:30 AM, Sunday, August 17, 2008 Sofitel -- Orleans, Oral

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