ZINC15:examples:screening - Revision history

Frodo: /* Physical-property-based screening libraries */ asdf

2015-10-16T22:00:02Z

Physical-property-based screening libraries: asdf

← Older revision		Revision as of 22:00, 16 October 2015
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	== Physical-property-based screening libraries ==		== Physical-property-based screening libraries ==
	ZINC is organized into physical property subsets for easier download of relevant tranches of physical-property chemical space. Please the tranche selection tool, [http://zinc15.docking.org/tranches/~~build/~~ http://zinc15.docking.org/tranches/home]		ZINC is organized into physical property subsets for easier download of relevant tranches of physical-property chemical space. Please the tranche selection tool, [http://zinc15.docking.org/tranches/home http://zinc15.docking.org/tranches/home]

	Do you want a 2D library (SMILES and their properties) for chemoinformatics or a 3D library for docking? Use the 2D/3D selector in the top left. We take up the two situations in turn.		Do you want a 2D library (SMILES and their properties) for chemoinformatics or a 3D library for docking? Use the 2D/3D selector in the top left. We take up the two situations in turn.

Frodo: asdf

2015-10-16T21:59:46Z

asdf

← Older revision		Revision as of 21:59, 16 October 2015
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	== Physical-property-based screening libraries ==		== Physical-property-based screening libraries ==
	ZINC is organized into physical property subsets for easier download of relevant tranches of physical-property chemical space. Please the tranche selection tool, [http://zinc15.docking.org/tranches/build/ http://zinc15.docking.org/tranches/~~build/~~]		ZINC is organized into physical property subsets for easier download of relevant tranches of physical-property chemical space. Please the tranche selection tool, [http://zinc15.docking.org/tranches/build/ http://zinc15.docking.org/tranches/home]

	Do you want a 2D library (SMILES and their properties) for chemoinformatics or a 3D library for docking? Use the 2D/3D selector in the top left. We take up the two situations in turn.		Do you want a 2D library (SMILES and their properties) for chemoinformatics or a 3D library for docking? Use the 2D/3D selector in the top left. We take up the two situations in turn.

Frodo: /* Chemotype-focused (ad hoc) screening library */

2015-05-08T19:01:05Z

Chemotype-focused (ad hoc) screening library

← Older revision		Revision as of 19:01, 8 May 2015
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	* 2. use a download script to specify format, purchasability, charge, pH range, and clean axis.		* 2. use a download script to specify format, purchasability, charge, pH range, and clean axis.

	Back to [[~~:Category:~~ZINC15:examples]]		Back to [[ZINC15:examples]]

	[[Category:ZINC15]]		[[Category:ZINC15]]
	~~[[Category:ZINC15:examples]]~~

Frodo: asdf

2015-05-08T19:00:25Z

asdf

New page

Two kinds of screening library we can think of.

== Physical-property-based screening libraries ==
ZINC is organized into physical property subsets for easier download of relevant tranches of physical-property chemical space. Please the tranche selection tool, [http://zinc15.docking.org/tranches/build/ http://zinc15.docking.org/tranches/build/]

Do you want a 2D library (SMILES and their properties) for chemoinformatics or a 3D library for docking? Use the 2D/3D selector in the top left. We take up the two situations in turn.

== Acquire a 2D library ==

1. use the preset menu (top right) to select the closest set of tranches to what you want
1a. Specify purchasability level (top left)
2. when ready, use the download button (top right) to download the tranches.
3. Within the download dialog box, if this is an incremental update, specify the last date you updated ZINC. Only tranches changed since then will be downloaded.
4. Only one format is allowed for 2D, SMILES.
5. In the method selector, chose from among four options.
a. URLs (default). One line per URL to be downloaded
b. DOCK Database Index, for local access, only makes sense at UCSF
c. cURL - script to use CURL
d. wget - script to use Wget.
6. When ready. click on download. This script must be then used to actually download the files.

== Acquire a 3D library for docking ==

1. use the preset menu (top right) to select the closest set of tranches to what you want
1a. Specify purchasability level (top left) pH range, Chemical filters and Charge, if desired (top).
2. when ready, use the download button (top right) to download the tranches.
3. Within the download dialog box, if this is an incremental update, specify the last date you updated ZINC. Only tranches changed since then will be downloaded.
4. Specify format. We support .db2.gx (DOCK 3.7) .db.gz (DOCK 3.6), .mol2.gz and .sdf.gz (many programs) and .pdbqt.gz (Autodock).
5. In the method selector, chose from among four options.
a. URLs (default). One line per URL to be downloaded
b. DOCK Database Index, for local access, only makes sense at UCSF
c. cURL - script to use CURL
d. wget - script to use Wget.
6. When ready. click on download. This script must be then used to actually download the files.

== Chemotype-focused (ad hoc) screening library ==

Two main steps are
* 1. get the ZINC IDs of the molecules you want
* 2. use a download script to specify format, purchasability, charge, pH range, and clean axis.

Back to [[:Category:ZINC15:examples]]

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