1. We made a change to DOCK Blaster that makes it generally more reliable against a wider range of targets. Thus there are now dozens of PDB structures that would previously crash due to various failures that will now run to completion. The results themselves are not any better (probably), but anecdotal tests suggest they are just as good.
2. We are aware of a bug when displaying the results of a DOCK Blaster run. The work around is to simply reload the page, by putting your cursor in the URL and hitting return. I know, we will fix it soon, but at least there is an easy work around.
We wanted to share some news: [Corrected and expanded version 1.1]
1. A new receptor protonation scheme was activated in DOCK Blaster today. The new code should be more robust. Expect results to be very slightly different. We will be monitoring this, and let you know. There is really no way to test it except to use it.
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.