About ZINC subsets - Revision history

Khtang: /* Subsets are broken into tranches for easier download */

2019-01-04T22:04:39Z

Subsets are broken into tranches for easier download

← Older revision		Revision as of 22:04, 4 January 2019
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	* [[mol2]] files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.		* [[mol2]] files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.
	* [[SDF]] files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.		* [[SDF]] files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.
	* [Flexibase_Format \| Flexibase] files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.		* [[Flexibase_Format \| Flexibase]] files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.

	= Shell scripts simplify download =		= Shell scripts simplify download =

Khtang: /* Subsets are broken into tranches for easier download */

2019-01-04T22:04:26Z

Subsets are broken into tranches for easier download

← Older revision		Revision as of 22:04, 4 January 2019
Line 15:		Line 15:
	* [[mol2]] files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.		* [[mol2]] files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.
	* [[SDF]] files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.		* [[SDF]] files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.
	* [[Flexibase]] files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.		* [Flexibase_Format \| Flexibase] files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.

	= Shell scripts simplify download =		= Shell scripts simplify download =

Frodo at 06:08, 13 March 2014

2014-03-13T06:08:08Z

← Older revision		Revision as of 06:08, 13 March 2014
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	For chemo-informatic projects, you may just want a <i>single</i> representation at pH 7		For chemo-informatic projects, you may just want a <i>single</i> representation at pH 7

			Back to [[:Category:ZINC\|ZINC]]
	[[Category:ZINC]]		[[Category:ZINC]]

Frodo: /* Subsets are broken into tranches for easier download */

2014-03-11T00:18:46Z

Subsets are broken into tranches for easier download

← Older revision		Revision as of 00:18, 11 March 2014
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	= Subsets are broken into tranches for easier download =		= Subsets are broken into tranches for easier download =

	* mol2 files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.		* [[mol2]] files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.
	* SDF files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.		* [[SDF]] files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.
	* Flexibase files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.		* [[Flexibase]] files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.

	= Shell scripts simplify download =		= Shell scripts simplify download =

Therese: 2 revisions

2012-10-08T18:10:25Z

2 revisions

← Older revision

Revision as of 18:10, 8 October 2012

Frodo at 16:49, 28 March 2012

2012-03-28T16:49:48Z

← Older revision		Revision as of 16:49, 28 March 2012
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	= Subsets are broken into tranches for easier download =		= Subsets are broken into tranches for easier download =

	* mol2 files: ~~100~~ MB uncompressed, about 23 MB compressed and about 20,000 molecules each on average.		* mol2 files: 700 MB uncompressed (CD size), about 127 MB compressed and about 120,000 molecules each on average.
	* SDF files: about ~~90MB~~ uncompressed, 16 MB compressed, about 20,000 molecules each on average.		* SDF files: about 542MB uncompressed, 90 MB compressed, about 120,000 molecules each on average.
	* Flexibase files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.		* Flexibase files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.

Frodo at 20:30, 2 December 2011

2011-12-02T20:30:16Z

New page

Some information about ZINC subsets

= Molecular formats =
Molecules are available in four formats: isomeric SMILES, mol2, SDF
and flexibase. Molecules are represented as a single pH=7 form (called reference or ref for short).
Additional representations (protonation variants and tautomers) are
available in three incremental subsets to augment the single representative:
* medium pH (6 to 8), probably desirable for most proteins
* high pH 8-9.5 (e.g. for docking to metals)
* and low pH 4.5-6 (e.g. for docking to a positively charged binding site, which in our experience is rare).

= Subsets are broken into tranches for easier download =

* mol2 files: 100 MB uncompressed, about 23 MB compressed and about 20,000 molecules each on average.
* SDF files: about 90MB uncompressed, 16 MB compressed, about 20,000 molecules each on average.
* Flexibase files: about 90MB uncompressed, 37 MB compressed. about 2000 hierarchies per file on average.

= Shell scripts simplify download =
For all but the smallest subsets, we recommend the use of a shell script to download the database.
For most docking projects, we recommend the Usual ligands: relevant forms between pH 6 and 8.
For docking to metalloenzymes, we recommend the Metal subsets, which includes high pH forms.
Note that these sets are overlapping so you do not want to download both Metals and All.
For chemo-informatic projects, you may just want a single representation at pH 7

[[Category:ZINC]]