Metabolites - Revision history

Frodo: ads

2015-10-02T03:50:57Z

ads

Frodo: asdf

2015-06-10T03:44:58Z

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← Older revision		Revision as of 03:44, 10 June 2015
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	[[Category:Metabolites]]		[[Category:Metabolites]]
	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]

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2015-06-10T00:47:50Z

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← Older revision		Revision as of 00:47, 10 June 2015
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	http://zinc15.docking.org/substances/subsets/endogenous+purchasable		http://zinc15.docking.org/substances/subsets/endogenous+purchasable
	To obtain a thousand of these in SDF form, use:		To obtain a thousand of these in SDF form, use:
	http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=~~100~~		http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=1000
	To find out which catalogs contribute to the endogenous subset of ZINC, use:		To find out which catalogs contribute to the endogenous subset of ZINC, use:
	http://zinc15.docking.org/catalogs/subsets/endogenous		http://zinc15.docking.org/catalogs/subsets/endogenous

Frodo: sadf

2015-06-10T00:42:10Z

sadf

← Older revision		Revision as of 00:42, 10 June 2015
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	http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100		http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100
	To find out which catalogs contribute to the endogenous subset of ZINC, use:		To find out which catalogs contribute to the endogenous subset of ZINC, use:
	http://zinc15.docking.org/~~catalots~~/subsets/endogenous		http://zinc15.docking.org/catalogs/subsets/endogenous
	If you believe a catalog has been incorrectly curated, please write us!		If you believe a catalog has been incorrectly curated, please write us!

Frodo: asdf

2015-06-09T18:07:01Z

asdf

← Older revision		Revision as of 18:07, 9 June 2015
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	If you have access to such a mapping, let us know and we can help you do the filtering you request.		If you have access to such a mapping, let us know and we can help you do the filtering you request.

	Turning to the questions more broadly raised in the email, we ~~image~~ our correspondent is		Turning to the questions more broadly raised in the email, we imagine our correspondent might be
	using "HMDB" as a proxy for "human metabolites". ~~This is not actually correct.~~ HMDB is a very powerful		using "HMDB" as a proxy for "endogenous human metabolites". In fact, HMDB is a very powerful
	resource that also includes drug metabolites, plant and food metabolites, ~~and~~ other xenobiotics. Fortunately,		resource that also includes drug metabolites, plant and food metabolites, among other xenobiotics. Fortunately,
	HMDB does break these different classes out, and we have categorized them separately in ZINC.		HMDB does break these different classes out, and we have categorized them separately in ZINC.

	Thus, to access only endogenous human metabolites from HMDB in ZINC, use:		Thus, to access only endogenous human metabolites from HMDB in ZINC, use:
	http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/purchasable		http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/purchasable

	~~But we wonder~~ whether our reader ~~was actually really~~ interested in endogenous human metabolites,		We wondered whether our reader might be interested in endogenous human metabolites more generally,
	not ~~only~~ in HMDB ~~but from any other public sources~~. ~~If so~~, we suggest using the ZINC endogenous subset, thus:		not just those in HMDB. Here, we suggest using the ZINC endogenous subset, thus:
	http://zinc15.docking.org/substances/subsets/endogenous+purchasable		http://zinc15.docking.org/substances/subsets/endogenous+purchasable
	To ~~get~~ a thousand of these in SDF form, ~~just do~~:		To obtain a thousand of these in SDF form, use:
	http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100		http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100
	~~Now, you may be wondering,~~ which catalogs contribute to the endogenous subset of ZINC~~. For this~~, ~~you would~~ use:		To find out which catalogs contribute to the endogenous subset of ZINC, use:
	http://zinc15.docking.org/catalots/subsets/endogenous		http://zinc15.docking.org/catalots/subsets/endogenous
	If you believe a catalog has been incorrectly curated, please write us!		If you believe a catalog has been incorrectly curated, please write us!

			Naturally, this analysis can be extended to other catalogs
			http://zinc15.docking.org/catalogs/
			and catalog subsets
			http://zinc15.docking.org/catalogs/subsets

	[[Category:Metabolites]]		[[Category:Metabolites]]
	[[Category:Tutorial]]		[[Category:Tutorial]]

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2015-06-09T18:01:19Z

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← Older revision		Revision as of 18:01, 9 June 2015
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	I was wondering if it is possible to download a purchasable subset of		I was wondering if it is possible to download a purchasable subset of
	HMDB (such that each molecule is purchasable (but without molecules		HMDB (such that each molecule is purchasable (but without molecules
	that are metabolites of purchasable ones, but not purchasable on ~~there~~ own)		that are metabolites of purchasable ones, but not purchasable on their own)

	We begin by doing the best we can on the question as asked, and then broaden the question:		We begin by doing the best we can on the question as asked, and then broaden the question:

Frodo: asdf

2015-06-09T18:00:48Z

asdf

← Older revision		Revision as of 18:00, 9 June 2015
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	Many people are interested in metabolites, including purchasable metabolites. We get emails such as this one:		Many people are interested in metabolites, including purchasable metabolites. We get emails such as this one:

	~~<snip>~~
	We are looking into HMDB for GPCR deorphanization tasks,		We are looking into HMDB for GPCR deorphanization tasks,
	and for practical purposes want to focus on purchasable molecules only.		and for practical purposes want to focus on purchasable molecules only.
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	HMDB (such that each molecule is purchasable (but without molecules		HMDB (such that each molecule is purchasable (but without molecules
	that are metabolites of purchasable ones, but not purchasable on there own)		that are metabolites of purchasable ones, but not purchasable on there own)
	~~</snip>~~

	We begin by doing the best we can on the question as asked, and then broaden the question:		We begin by doing the best we can on the question as asked, and then broaden the question:
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	Unfortunately, we do not keep track of which compounds are metabolites of other molecules.		Unfortunately, we do not keep track of which compounds are metabolites of other molecules.
	If you ~~had~~ access to such a ~~program~~, ~~then~~ we can help you.		If you have access to such a mapping, let us know and we can help you do the filtering you request.

	~~Now, turning~~ to the questions more broadly raised in the email, we image our correspondent is		Turning to the questions more broadly raised in the email, we image our correspondent is
	using "HMDB" as a proxy for "human metabolites". This is not actually correct. HMDB is a very powerful		using "HMDB" as a proxy for "human metabolites". This is not actually correct. HMDB is a very powerful
	resource that also includes drug metabolites, plant and food metabolites, and other xenobiotics. Fortunately,		resource that also includes drug metabolites, plant and food metabolites, and other xenobiotics. Fortunately,
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	Now, you may be wondering, which catalogs contribute to the endogenous subset of ZINC. For this, you would use:		Now, you may be wondering, which catalogs contribute to the endogenous subset of ZINC. For this, you would use:
	http://zinc15.docking.org/catalots/subsets/endogenous		http://zinc15.docking.org/catalots/subsets/endogenous
	If you ~~disagree about our~~ catalog ~~curation~~, please write us!		If you believe a catalog has been incorrectly curated, please write us!

	[[Category:Metabolites]]		[[Category:Metabolites]]
	[[Category:Tutorial]]		[[Category:Tutorial]]

Frodo: asdf

2015-06-09T17:56:43Z

asdf

New page

Many people are interested in metabolites, including purchasable metabolites. We get emails such as this one:

<snip>
We are looking into HMDB for GPCR deorphanization tasks,
and for practical purposes want to focus on purchasable molecules only.
I was wondering if it is possible to download a purchasable subset of
HMDB (such that each molecule is purchasable (but without molecules
that are metabolites of purchasable ones, but not purchasable on there own)
</snip>

We begin by doing the best we can on the question as asked, and then broaden the question:

To get the purchasable compounds in HMDB, you would use:
http://zinc15.docking.org/catalogs/hmdb/substances/subsets/purchasable
To download these in SMILES, you would just add .smi to the end, and say you want all of them, thus:
http://zinc15.docking.org/catalogs/hmdb/substances/subsets/purchasable.smi?count=all

Unfortunately, we do not keep track of which compounds are metabolites of other molecules.
If you had access to such a program, then we can help you.

Now, turning to the questions more broadly raised in the email, we image our correspondent is
using "HMDB" as a proxy for "human metabolites". This is not actually correct. HMDB is a very powerful
resource that also includes drug metabolites, plant and food metabolites, and other xenobiotics. Fortunately,
HMDB does break these different classes out, and we have categorized them separately in ZINC.

Thus, to access only endogenous human metabolites from HMDB in ZINC, use:
http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/purchasable

But we wonder whether our reader was actually really interested in endogenous human metabolites,
not only in HMDB but from any other public sources. If so, we suggest using the ZINC endogenous subset, thus:
http://zinc15.docking.org/substances/subsets/endogenous+purchasable
To get a thousand of these in SDF form, just do:
http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100
Now, you may be wondering, which catalogs contribute to the endogenous subset of ZINC. For this, you would use:
http://zinc15.docking.org/catalots/subsets/endogenous
If you disagree about our catalog curation, please write us!

[[Category:Metabolites]]
[[Category:Tutorial]]

← Older revision		Revision as of 03:50, 2 October 2015
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	To get the purchasable compounds in HMDB, you would use:		To get the purchasable compounds in HMDB, you would use:
	http://zinc15.docking.org/catalogs/hmdb/substances/subsets/~~purchasable~~		http://zinc15.docking.org/catalogs/hmdb/substances/subsets/for-sale
	To download these in SMILES, you would just add .smi to the end, and say you want all of them, thus:		To download these in SMILES, you would just add .smi to the end, and say you want all of them, thus:
	http://zinc15.docking.org/catalogs/hmdb/substances/subsets/~~purchasable~~.smi?count=all		http://zinc15.docking.org/catalogs/hmdb/substances/subsets/for-sale.smi?count=all

	Unfortunately, we do not keep track of which compounds are metabolites of other molecules.		Unfortunately, we do not keep track of which compounds are metabolites of other molecules.
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	Thus, to access only endogenous human metabolites from HMDB in ZINC, use:		Thus, to access only endogenous human metabolites from HMDB in ZINC, use:
	http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/~~purchasable~~		http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/for-sale

	We wondered whether our reader might be interested in endogenous human metabolites more generally,		We wondered whether our reader might be interested in endogenous human metabolites more generally,
	not just those in HMDB. Here, we suggest using the ZINC endogenous subset, thus:		not just those in HMDB. Here, we suggest using the ZINC endogenous subset, thus:
	http://zinc15.docking.org/substances/subsets/endogenous+~~purchasable~~		http://zinc15.docking.org/substances/subsets/endogenous+for-sale
	To obtain a thousand of these in SDF form, use:		To obtain a thousand of these in SDF form, use:
	http://zinc15.docking.org/substances/subsets/endogenous+~~purchasable~~.sdf?count=1000		http://zinc15.docking.org/substances/subsets/endogenous+for-sale.sdf?count=1000
	To find out which catalogs contribute to the endogenous subset of ZINC, use:		To find out which catalogs contribute to the endogenous subset of ZINC, use:
	http://zinc15.docking.org/catalogs/subsets/endogenous		http://zinc15.docking.org/catalogs/subsets/endogenous