We have begun creating how-to videos for docking.org software, focusing first on the new version of ZINC. Sorry about the ads, they pay for the service.
All ZINC subsets (lead like, fragment like, clean leads, leads now, all purchasable etc) have been updated except for drug like, which is still in progress.
We aim to update all subsets quarterly or better, and some subsets are updated monthly.
For you pentadactyls who still haven't given up facebook, our ZINC group http://facebook.com/zincdb just hit 100 members. Whoo hoo! Tell your friends.
ZINC offers a range of database subsets to suit a range of research objectives. We ourselves use the "lead like" and "fragment like" subsets most often (#1 and #2).
Some of our colleagues use "drug like" or "all purchasable" subsets. We frankly find those molecules too big for docking, but we do understand that they have their uses - that is why they exist (#3 and #6).
DOCK Blaster is back. Changes include: 1) better decoys. 2) better geometries 3) better energies. 4) better treatment of ligand desolvation.
#4 is in Mysinger and Shoichet, JCIM, 2010.
#1 is in Mysinger, Irwin, Shoichet, man in prep
#2 and #3 will probably be Mysinger and Koovakkat, to be published.
There are more #2 and #3 changes coming in the next month. stay tuned.
Dear DOCK Blaster Users
We are having some difficulties arising from a software upgrade to DOCK Blaster yesterday. Basically, most jobs are not running correctly. We are working to fix this problem as quickly as we can. Please stand by.
ZINC, SEA, DUD and other services should be unaffected.
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.
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).
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.