Category:ZINC: Difference between revisions

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The ZINC Database contains commercially available compounds for structure based virtual screening. It currently has about '''over 1 billion compounds that can simply be purchased'''.  It is provided in ready-to-dock, 3D formats with molecules represented in biologically relevant forms. It is available in subsets for general screening as well as target-, chemotype- and vendor-focused subsets.  ZINC is free for everyone to use and download at the [http://zinc15.docking.org website].  This database and service is provided by the [[Shoichet Lab | Shoichet Laboratory]] in the [[Department of Pharmaceutical Chemistry]] at the [[University of California San Francisco]] (UCSF). 
Here contains subcategories & pages about [[ZINC]] database


To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman,
== Current versions ==
J. Chem. Inf. Model. 2012.
There are two versions of ZINC that are current:  
[http://pubs.acs.org/doi/abs/10.1021/ci3001277 | DOI: 10.1021/ci3001277 ]
* [[ZINC20]] - the successor to ZINC15 that contains all of its features, and is updated.  
* [[:Category:ZINC22 | ZINC22]] - a database that focuses on size and uses mostly make-on-demand molecules.


To cite the original ZINC paper, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82
==Legacy versions (as of 05/2024)==
[http://pubs.acs.org/doi/abs/10.1021/ci049714 | DOI: 10.1021/ci049714 ]. We thank [http://www.nigms.nih.gov/ NIGMS] for financial support (GM71896).
* [[:Category:ZINC15 | ZINC15]] - Our '''current''' version of the [[ZINC]] database, release to public since late 2015. It is on [http://zinc15.docking.org zinc15.docking.org]
* [[ZINC12]] - Still available on [http://zinc.docking.org zinc.docking.org] but is no longer supported since 2015.
* [[ZINC:History]]
==What is included in ZINC?==
* [[About ZINC subsets ]]
* [[ZINC Biogenic Libraries]]
* [[ZINC subsets]]
* [[Metabolites databases]]
* [[XML RPC Services]]
* [[Blacklist]]
==Tutorials==
===For website users===
===For command line users===


'''[[ZINC15]] is the most current version of ZINC.'''  The prior version was [[:Category:ZINC12 | ZINC12]].
== Purpose ==
ZINC was originally designed for target based virtual screening (docking), and this remains its primary focus. However, ZINC is also useful for many other things, including:
* finding a compound to purchase
* downloading a library in SMILES format for [[ligand based virtual screening]]
* find compounds by similarity to a starting compound (SAR-by-catalog)
* find compound ANNOTATED for a particular target (via ChEMBL)
* find compounds PREDICTED for a particular target (via SEA / ChEMBL or docking)
* and much more...
== Scope ==
ZINC includes over 400 catalogs from over 300 vendors and over 100 annotated catalogs.  A list of all purchasable catalogs used is [http://zinc15.docking.org/catalogs/subsets/for-sale/].  A list of all annotated (non-purchasable) catalogs is [http://zinc15.docking.org/catalogs/subsets/annotated].  Purchasable bioactive compounds, that is, molecules that are purchasable drawn from non-purchasable annotated catalogs are [http://zinc15.docking.org/catalogs/subsets/bioactive+purchasable].  ZINC also contains catalogs of [http://zinc15.docking.org/catalogs/subsets/biogenic+purchasable].
== Access ==
ZINC may be accessed at [http://zinc15.docking.org/  zinc15.docking.org].  ZINC is freely available to everyone to use.  Significant portions of ZINC may not be re-distributed without express written permission of John Irwin.
== Curation ==
ZINC is curated by the [[ZINC Curators]].  This group works to improve and maintain the database, and to keep it as current as possible.
== Updates ==
ZINC is updated continuously. In a typical week:
* 100,000 new molecules are loaded
* 10,000 molecules are repaired
* 80,000 catalog items are marked "depleted" due to their absence from the most current catalogs.
* 3 new catalogs are added.
* 30 tranches of the 2D and 3D property subsets are updated.
== Use ==
ZINC is widely used. We receive over 500 unique visitors per day, 13,000 per month, and have over 50,000 "repeat customers".
== Formats ==
ZINC is available in [[SMILES]], [[mol2]], [[SDF]], [[pdbqt]], and [[Flexibase Format | flexibase]] formats.
== What is ZINC not? ==
===Not every molecule for sale===
It focuses on biologically relevant compounds.  To achieve this focus, ZINC filters out molecules widely considered unsuitable for docking, such as peroxides, big insoluble molecules, large peptides, and highly reactive reagents including many building blocks. See our [http://filtering.docking.org filtering rules]. We also filter out molecules containing metals, boron, and silicon, because there are no MMFF94 parameters for these atoms.
===Not all drugs===
Some filtered compounds, such as cis-platin, are actually drugs or drug candidates. Our focus is on virtual screening and molecular modeling, something we do not know how to do with cis-platin, or boronic acids.  For general purpose purchasing, we suggest [http://chemspider.com chemspider.com] or [http://emolecules.com emolecules.com].
===Not encyclopedic===
ZINC is single minded in its focus on biologically relevant representations of molecules.  It does not keep track of many other kinds of information, such as CAS numbers, or even names.  For these, please try [http://www.chemdb.com/ ChemDB], [http://pubchem.ncbi.nlm.nih.gov/ PubChem], [http://www.drugbank.ca/ DrugBank], [http://biocyc.org/ biocyc/metacyc], [http://www.ebi.ac.uk/chembl/ ChEMBL], [http://chemspider.com ChemSpider], along with many others.
== Version ==
We differentiate the website software and the version of any particular subset that is downloaded.  The current version of the website software is 15, that became beta in June 2015 and was officially released later in 2015.  For more information, please see [[ZINC:History]].
When referring to a subset that is downloaded from ZINC (for instance, "lead like" or "fragment like"), each tranche has a date of preparation and a count of the number of unique molecules in the subset, which are often only approximate within about 1%.  Subsets are static version of a dynamically changing database.  Thus when referring to a ZINC subset in a publication, we recommend saying, "The lead-like subset containing 7,123,456 unique molecules was downloaded on 20 Nov 2015"  (for instance).
== Recommended usage ==
For most prospective docking projects, we recommend you download the "lead like" or "fragment like" subsets of ZINC in the format closest to the one used by your docking program (e.g. mol2, SDF, pdbqt).  We recommend that you download the supplier information at the same time, so that you have a permanent mapping from ZINC ID numbers to original supplier codes.  From time to time molecules disappear from ZINC, usually due to depletion, so downloading static supplier information means you do not depend on looking up compounds on the database in the future.
There are other applications and uses of ZINC, but this is in our view by far the most common and useful application.
== Which suppliers are included? ==
Please see the [http://zinc15docking.org/catalogs] page. If there is a catalog you would like to see loaded, please write to databases at docking.org.
== Filtering rules ==
ZINC is loaded from commercial supplier catalogs and annotated databases. '''We only load molecules we feel will be useful for virtual screening.'''
<div class="toccolours mw-collapsible mw-collapsed">
'''Read more'''
<div class="mw-collapsible-content">
* For commercial compounds, we do not load highly reactive compounds, or compounds over 500 g/mol.
* For annotated compounds and vendor catalogs of bioactives which are often drugs, metabolites, natural products or natural derivatives, we relax these constraints to allow up to 600g/mol and we allow some reactive functional groups that would otherwise not be considered acceptable for screening.
* For make-on-demand compounds, we may only load only up to 400 g/mol.
* Some make-on-demand and agent catalogs are incompletely loaded, deliberately.  We need to upgrade our hardware and software first.
Our rules do change as our thinking evolves.  The current rules are available in textual and graphical form at [http://filtering.docking.org filtering.docking.org] {LINK NO LONGER WORKING}.  If you disagree with choices we have made, we would be happy to discuss them with you in our [http://docking.org/forum/14 Forum] {LINK NO LONGER WORKING}.
To see the filtering rules in effect in ZINC, please see  [http://filtering.docking.org filtering.docking.org] {LINK NO LONGER WORKING}.
We filter both at load time and also at subset preparation time. Molecules are not loaded if:
* They do not pass our load-time filtering criteria
* An error occurs during processing.
Each filtered-out compound is justified with a reason, available via the vendor page.  Every compound in every supplier catalog we load has one of four fates:
* It loaded and visible in ZINC.
* It is depleted (not longer available) - and may still be in ZINC, marked depleted. Depleted compounds may not persist for long.
* It was filtered out and never loaded. These are listed as "filtered out" on the vendor pages.
* It failed at some stage of processing, and may appear nowhere except in the original vendor catalog.
</div>
</div>
[[Filtering Rules]]
== External Links ==
* [http://zinc15.docking.org ZINC database]
* [http://zincpharmer.csb.pitt.edu ZINCPharmer] An online pharmacophore search tool from the University of Pittsburgh
* [http://facebook.com/zincdb ZINC Facebook page contains links to sites that use ZINC]
== Problems with ZINC ==
ZINC has many problems. Please see our [[feedback]] page on how to tell us about problems.
== How do subsets work? ==
We have pre-made subsets ([http://zinc15.docking.org/catalogs], by [http://zinc15.docking.org/tranches], and
[http://zinc.docking.org/browse/subsets/special.php special properties])
that we hope you find useful and may well satisfy many if not most of your needs.
We also offer subsets
[http://zinc.docking.org/browse/targets/ by target], annotated by binding, functional activity, or ADME/T activity via ChEMBL.
We also allow you to download the results of any search, up to 1000 molecules.  You can also collect molecules in the shopping cart, and then download those in any format we support.
You may also upload your own molecules, either as SMILES of ZINC IDs, into a shopping cart, and then download those in any format we support.
You may also create decoys based on the molecules in the shopping cart, and download those.
[[About ZINC subsets]]
= See Also =
* [[ZINC numbers]]
* [[Community_Portal]]
* [[ZINC:Command_language]]
* [[XML_RPC_Services]]
[[Category:ZINC]]
[[Category:Topic]]
[[Category:Topic]]
[[Category:Free]]
[[Category:Free]]
[[Category:Databases]]
[[Category:Databases]]

Revision as of 15:38, 29 April 2024

Here contains subcategories & pages about ZINC database

Current versions

There are two versions of ZINC that are current:

  • ZINC20 - the successor to ZINC15 that contains all of its features, and is updated.
  • ZINC22 - a database that focuses on size and uses mostly make-on-demand molecules.

Legacy versions (as of 05/2024)

What is included in ZINC?

Tutorials

For website users

For command line users

Subcategories

This category has the following 2 subcategories, out of 2 total.

Z

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