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 | The ZINC Database contains commercially available compounds for structure based virtual screening. It currently has about 90 million 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 website [http://zinc.docking.org zinc.docking.org]. 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). | ||
To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman, | To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman, | ||
J. Chem. Inf. Model. 2012 | J. Chem. Inf. Model. 2012. | ||
[http://pubs.acs.org/doi/abs/10.1021/ci3001277 | DOI: 10.1021/ci3001277 ] | [http://pubs.acs.org/doi/abs/10.1021/ci3001277 | DOI: 10.1021/ci3001277 ] | ||
To cite the original ZINC paper, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank [http://www.nigms.nih.gov/ NIGMS] for financial support (GM71896). | To cite the original ZINC paper, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank [http://www.nigms.nih.gov/ NIGMS] for financial support (GM71896). | ||
'''ZINC15 is in the process of being released as a new version of ZINC''' The prior version was ZINC12. | |||
* [[ZINC15]] | |||
* [[ZINC12]] | |||
{{TOCright}} | {{TOCright}} | ||
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= Scope = | = Scope = | ||
ZINC includes over | 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/purchasable]. 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 = | = Access = | ||
ZINC may be accessed at [http:// | 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 = | = Curation = | ||
| Line 31: | Line 35: | ||
ZINC is updated continuously. In a typical week: | ZINC is updated continuously. In a typical week: | ||
* | * 100,000 new molecules are loaded | ||
* 10,000 molecules are repaired | * 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 = | = Use = | ||
ZINC is widely used. We receive | ZINC is widely used. We receive over 500 unique visitors per day, 13,000 per month, and have over 50,000 "repeat customers". | ||
= Formats = | = Formats = | ||
ZINC is available in [[SMILES]], [[mol2]], [[SDF]] and [[Flexibase Format | flexibase]] formats. | ZINC is available in [[SMILES]], [[mol2]], [[SDF]], [[pdbqt]], and [[Flexibase Format | flexibase]] formats. | ||
= What is ZINC not? = | = What is ZINC not? = | ||
| Line 54: | Line 59: | ||
= Version = | = Version = | ||
We differentiate the website software and the version of any particular subset that is downloaded. The current version of the website software is | 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 will be 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 | 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 = | = 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. | 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. | 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? = | = Which suppliers are included? = | ||
Please see the | 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. | ||
[http:// | |||
= Filtering rules = | = Filtering rules = | ||
| Line 76: | Line 75: | ||
= External Links = | = External Links = | ||
* [http:// | * [http://zinc15.docking.org ZINC database] | ||
* [http://zincpharmer.csb.pitt.edu ZINCPharmer] An online pharmacophore search tool from the University of Pittsburgh | * [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] | * [http://facebook.com/zincdb ZINC Facebook page contains links to sites that use ZINC] | ||
= Problems with ZINC = | = Problems with ZINC = | ||
ZINC has many problems. Please see our [[feedback]] page on how to tell us about problems. | |||
= How do subsets work? = | = How do subsets work? = | ||
We have pre-made subsets ([http:// | 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]) | [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. | that we hope you find useful and may well satisfy many if not most of your needs. | ||
Revision as of 06:57, 3 June 2015
The ZINC Database contains commercially available compounds for structure based virtual screening. It currently has about 90 million 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 website zinc.docking.org. This database and service is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California San Francisco (UCSF).
To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman, J. Chem. Inf. Model. 2012. | DOI: 10.1021/ci3001277
To cite the original ZINC paper, please reference: Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank NIGMS for financial support (GM71896).
ZINC15 is in the process of being released as a new version of ZINC The prior version was 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 [1]. A list of all annotated (non-purchasable) catalogs is [2]. Purchasable bioactive compounds, that is, molecules that are purchasable drawn from non-purchasable annotated catalogs are [3]. ZINC also contains catalogs of [4].
Access
ZINC may be accessed at 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 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 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 chemspider.com or 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 ChemDB, PubChem, drugbank.ca, biocyc/metacyc, ChEMBL, chemspider.com, 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 will be 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 [5] page. If there is a catalog you would like to see loaded, please write to databases at docking.org.
Filtering rules
External Links
- ZINC database
- ZINCPharmer An online pharmacophore search tool from the University of Pittsburgh
- 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 ([6], by [7], and special properties) that we hope you find useful and may well satisfy many if not most of your needs.
We also offer subsets 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.
See Also
Subcategories
This category has the following 2 subcategories, out of 2 total.
Pages in category "ZINC"
The following 33 pages are in this category, out of 33 total.