THC - Revision history

Therese: 12 revisions

2012-10-08T20:33:12Z

12 revisions

← Older revision

Revision as of 20:33, 8 October 2012

2010-09-07T23:40:09Z

← Older revision		Revision as of 23:40, 7 September 2010
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	The top hits collection (THC) links indications, targets, and molecules. It contains information ranging from experimentally confirmed to speculative. The goal is to provide biologists with suggestions of small molecules that may be useful to modulate biology. THC is a community curated database. You are invited to contribute. Please see [[THC:community participation]] to learn more.		The top hits collection (THC) links indications, targets, and molecules. It contains information ranging from experimentally confirmed to speculative. The goal is to provide biologists with suggestions of small molecules that may be useful to modulate biology. THC is a community curated database. You are invited to contribute. Please see [[THC:community participation]] to learn more.

			= How to Use =
			THC is designed to be simple. You may search using indications, targets or molecules. You can display linked indications, targets, or molecules. You may also simply browse the database, or pick molecules at random.

			(more detail needed here)

	= Sources of Molecule-Target Assocations =		= Sources of Molecule-Target Assocations =

2010-09-07T23:28:55Z

3rd party user annotations

← Older revision		Revision as of 23:28, 7 September 2010
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	* [http://blaster.docking.org/ http://blaster.docking.org/]		* [http://blaster.docking.org/ http://blaster.docking.org/]

	== 3rd party user annotations ==		== 3rd party user annotations ==

			You may register at this site and upload your own data to THC. You may also comment on data that have been uploaded by other users. If at all possible, please support your data with links to publications (PMID #) or upload relevant spectra or other data to this wiki.

	= Sources of Indication-Target Assocations =		= Sources of Indication-Target Assocations =

2010-09-07T23:27:18Z

DOCK Blaster

← Older revision		Revision as of 23:27, 7 September 2010
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	== DOCK Blaster ==		== DOCK Blaster ==

			DOCK Blaster predicts small molecule binding to protein targets. The protein models are drawn from the PDB, and later from ChEMBL. Crucially, DOCK Blaster assesses the quality of the docking based on retrospective analysis, when ligands are available. When no control ligands are available, DOCK Blaster will attempt to assess docking reliablity in other ways.


			* [http://blaster.docking.org/ http://blaster.docking.org/]

	== 3rd party user annotations ==		== 3rd party user annotations ==

2010-09-07T23:24:50Z

SEA

← Older revision		Revision as of 23:24, 7 September 2010
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	* [http://www.ncbi.nlm.nih.gov/pcassay http://www.ncbi.nlm.nih.gov/pcassay]		* [http://www.ncbi.nlm.nih.gov/pcassay http://www.ncbi.nlm.nih.gov/pcassay]

	== SEA ==		== SEA ==


			Formerly called WINC, these are predictions made by SEA against all purchasable molecules (ZINC) based on publicly available data (ChEMBL).

			* [http://sea.docking.org/ http://sea.docking.org/]

	== DOCK Blaster ==		== DOCK Blaster ==

2010-09-07T23:23:55Z

PubChem Assay

← Older revision		Revision as of 23:23, 7 September 2010
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	* [http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html]		* [http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html]

	== PubChem Assay ==		== PubChem Assay ==

			On the one hand, there is a lot of data in here. On the other hand, the data are very noisy, perhaps so noisy as to be useless. Still, we can tell our user about this data, and let him or her decide about it, by linking back to the original source.

			* [http://www.ncbi.nlm.nih.gov/pcassay http://www.ncbi.nlm.nih.gov/pcassay]

	== SEA ==		== SEA ==

2010-09-07T23:22:42Z

FDA Orange Book

← Older revision		Revision as of 23:22, 7 September 2010
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	completely subsumed in ChEMBL? not quite...		completely subsumed in ChEMBL? not quite...

	== FDA Orange Book ==		== FDA Orange Book ==

			EPA MDD is the SDF file we used. Contains mappings between drugs and indications.

			* [http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html]

	== PubChem Assay ==		== PubChem Assay ==

2010-09-07T23:21:48Z

Drugbank.ca

← Older revision		Revision as of 23:21, 7 September 2010
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	== Drugbank.ca ==		== Drugbank.ca ==

			This is another freely available source of information. It has molecule-target and molecule-indication mappings, and thus implicitly target-indication mappings.

			* [http://drugbank.ca/ http://drugbank.ca/]

	== bindingdb.org ==		== bindingdb.org ==

2010-09-07T23:20:46Z

ChEMBL

← Older revision		Revision as of 23:20, 7 September 2010
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	== ChEMBL ==		== ChEMBL ==
	This is the premier source of freely available medicinal chemistry information.		This is the premier source of freely available medicinal chemistry information. We are currently using ChEMBL 05 (August 2010).

			* [http://www.ebi.ac.uk/chembl/ http://www.ebi.ac.uk/chembl/]

	== Drugbank.ca ==		== Drugbank.ca ==

2010-09-07T23:06:04Z

@@ Line 1: / Line 1: @@
-The top hits collection is a collection of top hits against many targets as produced by [[DOCK Blaster]].
+The top hits collection (THC) links indications, targets, and molecules.   It contains information ranging from experimentally confirmed to speculative. The goal is to provide biologists with suggestions of small molecules that may be useful to modulate biology. THC is a community curated database.  You are invited to contribute.  Please see [[THC:community participation]] to learn more.
-THC is automatically generated, and then [[curated]] by experts.
 * [http://thc.docking.org THC Website]