Blogs

blog back up - sorry for the interruption

Dear docking.org fans

We were seeing a lot of hacking attempts, so I tightened up security in a bit of a panic. Unfortunately, I also broke this blog. Now that my paper is submitted and I am returning to other things, I have fixed the blog.

I am rededicating myself to making things better. We have a lot of new tools, released or soon to be released, and I will be telling you about them here.

John

power outage tonight Mon Nov 21 pm - Tues Nov 22 am

Dear docking.org users

We are having a building powerdown tonight. Some of our services may go offline. They will be re-started tomorrow morning (Tuesday) by 10am San Francisco time.

-- John

WHY ZINC 12 NOT SHOWS HOW MANY HITS ARE THERE FOR STRUCTURE OR PROPERTY SEARCH, AS WELL AS REFRESH TAB NOT DOWNLOADING ANY THNG

DEAR SIR
I M TRYING TO SEARCH ON ZINC 12 WITH STRUCTURE QUERY OF VORNINOSTAT , ITS SHOWS NO RESULT,
PROPERTY BASED RESULT DISPLAYED BUT DIFFICULT TO DOWNLOAD , AS WELL AS THERE IS NO OPTION HOW MANY HITS GOT THE QUERY ,
HOW CAN I DOWNLOAD ALL THE RESULT IN MOL2 OR OTHER FORMAT ,EACH TIME I REFRESH AFTER SELECTING MOL2 ,NUMBERS DISPLAYED ON THE SCREEN BUT NOTHING DOWNLOADED.SAME IS HAPPENING COMBINED SEARCH OPTION .

I TRIED ZINC 15 ITS STRUCTURE SEARCH WORK VERY GOOD BUT HOW TO COMBINE IT WITH LIPINSKEY RULE OR OUR CRITERIA PLZ LET ME KNOW THE SOLUTION, I WILL BE HIGHLY THANKFUL TO U.

Download ZINC15 by catalog

Dear ZINC Fans

An important missing feature in ZINC15 has been the ability to download dockable libraries by catalog.

Today, we are announcing a new feature that gives you a lot of flexibility to download 3D models for docking.

Please read more here: http://files.docking.org/catalogs/

We are preparing the files in increasing order of size. All small catalogs < 100,000 molecules are ready. We expect catalogs under 1,000,000 molecules will be ready by the weekend. Larger catalogs will take longer.

Please
* consider using libraries by property (the Tranche Browser)

fine chemicals

(S)​-​(-​)​-​1-​Amino-​2-​(methoxymethyl)​pyrrolidine 59983-39-0
1-Methyl-4-nitro-1h-pyrazole 3994-50-1
Cyclopropyl boronic acid 411235-57-9
4-Hydroxybutyric Acid Methyl Ester 925-57-5
3H-Indazol-3-one,5-bromo-1,2-dihydro 7364-27-4
1-Methyl-1H-indazol-5-ol 756839-14-2
5-Chloro-2-methyl-1h-pyrrolo[2,3-c]pyridine 905455-16-5
5-Chloro-2-methyl-1h-pyrrolo[2,3-c]pyridine 905455-16-5
2-AMINO-5-METHYL PYRIDINE 1603-41-4
(S)​-​(-​)​-​1-​Phenylethanol 1445-91-6
(4-methylphenyl)methanesulfonyl chloride 51419-59-1
5-fluoropyrimidine-2-carboxaldehyde 935667-50-8

ZINC 3D updated

Dear Dockers

We are announcing today a major update of the 3D docking libraries in ZINC15, accessible via the Tranche Browser: http://zinc15.docking.org/tranches/home/

The following numbers of molecules are available in ready to dock formats as follows: stock / on-demand / boutique

Lead-like: 2.9M / 52M / 56M
Fragment-like: 795K / 6.8M / 8.1M
Drug-like: 7.8M / 69M / 74M
All: 8.7M / 70M / 76M

There's more. We expect ZINC 3D lead like to grow by an average of 5 M per week for the rest of 2016.

Thank you for your interest in ZINC.

John

ZINC15 bigger than ever

ZINC15 has been updated.
The 2D version (SMILES) is ready for download.

A few highlights:
13 million compounds in stock, 233 M including make-on-demand and 331 M including boutique.

Leads: 3.4 M stock, 93 M including on demand, 133 M including boutique.

Fragments: 824 K in stock, 7M including on demand and 24 M including boutique.

We will be updating the 2D tranches continuously going forward. We will announce substantial revisions.

The 3D updates will be available later this month. "very soon".

http://zinc15.docking.org/tranches/home/

John

Dock file format

¿What can be done if you what to use the output files of Dock3.5 in Dock6.7? I am having trouble with the file type. Dock 6.7 just accepts .mol2 files but the output files of Dock3.5 are given in .pdb ¿What can I do to transform .pdb to .mol2 files?

Molecular excipients

Dear All

We have created a new tool for research in the area of molecular excipients.

We have just published a paper about it.
https://www.ncbi.nlm.nih.gov/pubmed/27557422

The website is online and ready to use:
http://excipients.ucsf.bkslab.org

This work is sponsored by the US Food and Drug Administration (FDA).

We're happy to talk to you if you have any questions about this new facility.

We hope you find it useful.

-- John

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