We help you discover chemistry for your biological targets.

DOCK Blaster grid preparation just got better, but also slower

Dear DOCK Blaster Users:

We released today a new method of grid preparation based on work that was published last year:

Mysinger MM, Shoichet BK., Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model. 2010 Sep 27;50(9):1561-73. The link is here: http://www.ncbi.nlm.nih.gov/pubmed/20735049

Our research shows that this produces better scoring grids for desolvation, but it also takes about 30-40 minutes to run instead of 10-15 minutes, typically.

Purchasable Bioactives is the new name for Oxymoronecules

We have re-christened Oxymoronecules as "Purchasable Bioactives" or Purchasable Bioactive Compounds (PBCs). We feel this is a more descriptive name of what they really are: compounds with experimentally known biological activity that are for sale.

Purchasable Bioactives includes biogenic molecules such as metabolites (HMDB, Metacyc) and natural products (TCM), drugs and experimental compounds (Drugbank, FDA), and bioactives from the medicinal chemistry literature (ChEMBL, BindingDB).

UCSF DOCK 6.5 now available

We are pleased to announce the release of DOCK 6.5.

DOCK is a suite of programs for molecular docking.
In version 6.5 a new scoring function Descriptor Score is available.
It reports van der Waals and Coulombic energies, hydrogen bonds, and
per-residue energy decomposition comparisons with a reference molecule.
DOCK continues to provide a variety of other scoring methods including
grid based, PB/SA, and GB/SA, as well as a simple interface to
the AmberTools MD engine that enables receptor flexibility and
a complete MM force field.

New ZINC subsets released week ending July 16th, 2011

Dear ZINC fans

We update ZINC continuously, about 5K to 10K new compounds per day. We re-generate ready-to-download subsets continuously too, but there are a lot of them, so we aim for quarterly for our most popular subsets. For our own work, we use almost exclusively the "lead like" and "fragment like" subsets.

Recently the following subsets have been created.
Lead-like (#1) now 3.06 M
Fragment-like (#2) now 367K

Immediate availability subsets:
Leads-now (#21) now 1.4 M
Drugs-now (#23) now 5.6 M
Frags-now (#22) now 300K

Annotated subsets


New SEA server released, http://sea.bkslab.org/

Dear SEA-fans

We have released a new version of the SEA website, http://sea.bkslab.org/, incorporating ChEMBL Version 10. Finally, the general public may now use SEA and see (ha ha) the annotated compounds from ChEMBL that were used to make the prediction.

Please give it a try!

John Irwin
for the SEA Development Team

ZINC has a facebook group

Please like our facebook group. We are highlighting uses of ZINC we find in the literature there. You are welcome to contribute too!


Targets from the lab

Here are the publicly available lists currently available:

Name: Wunschzettel
Description: This is my wish list

Decoymaker problem May 16 - May 23

Dear DOCK Blaster and Decoymaker (decoyprot) users:

We discovered a trivial yet critical problem in the decoy maker today (I forgot to reset the file permissions when I updated the file). This has been fixed.

What this means is that for any DOCK Blaster job run from May 16 - a few minutes ago (May 23), the decoymaker part of the DOCK Blaster toolchain was not working. Docking worked, but the decoys would hang, and this meant effectively that DOCK Blaster was broken for most applications.

Recently updated vendors in ZINC

The following vendor catalogs were updated in April.

* Life Chemicals Screening and Building Blocks
* Enamine Building Blocks
* Otava
* InterBioScreen screening, building blocks and bioactives
* ChemBridge Screening and Building Blocks
* Ambinter
* Shanghai Sinofluoro Scientific
For more info, see http://zinc.docking.org/vendor0/

We have also updated several non-commercial catalogs: (you cannot order from these sources)
* MLSMR4 - current version of the MLSMR in dockable form
* Collaborative Drug Discovery
* BindingDB.org
* PubChem

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