Decoys - Revision history

Teague Sterling at 18:38, 15 September 2015

2015-09-15T18:38:53Z

← Older revision		Revision as of 18:38, 15 September 2015
Line 42:		Line 42:
	Donors: 1 (==) → hbd=1		Donors: 1 (==) → hbd=1
	Acceptors: 2 (==) → hba=2		Acceptors: 2 (==) → hba=2
	Charge: 0 (==) → ~~charge~~=0		Charge: 0 (==) → net_charge=0
	Rotatable Bonds: 1 (==) → rb=1		Rotatable Bonds: 1 (==) → rb=1

	As a ZINC query these constraints would be:		As a ZINC query these constraints would be:

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&~~charge~~=0&rb=1>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&net_charge=0&rb=1>

	This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no		This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&~~charge~~=0&rb=1&count=50parallelize=no&distinct=no>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&net_charge=0&rb=1&count=50parallelize=no&distinct=no>

	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Teague Sterling: /* Getting Decoys for a SMILES (e.g. not in ZINC) */

2015-09-15T18:37:34Z

Getting Decoys for a SMILES (e.g. not in ZINC)

← Older revision		Revision as of 18:37, 15 September 2015
Line 47:		Line 47:
	As a ZINC query these constraints would be:		As a ZINC query these constraints would be:

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-~~unsorted-tanimoto~~-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1>

	This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no		This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-~~unsorted-tanimoto~~-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1&count=50parallelize=no&distinct=no>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1&count=50parallelize=no&distinct=no>

	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Teague Sterling at 18:32, 15 September 2015

2015-09-15T18:32:55Z

← Older revision		Revision as of 18:32, 15 September 2015
Line 37:		Line 37:
	Molecular Properties (Criteria) → URL Parameters:		Molecular Properties (Criteria) → URL Parameters:

	SMILES: CN(C)C(=O)c1ccc(O)cc1 (ECFP4-tanimoto < 0.25) → ~substance.ecfp4_fp-~~tanimoto~~=CN(C)C(=O)c1ccc(O)cc1		SMILES: CN(C)C(=O)c1ccc(O)cc1 (ECFP4-tanimoto < 0.25) → ~substance.ecfp4_fp-unsorted_tanimoto-25=CN(C)C(=O)c1ccc(O)cc1
	MWT: 165.2 (+/- 10%) → mwt-between=148.67,181.72		MWT: 165.2 (+/- 10%) → mwt-between=148.67,181.72
	LogP: 1.1 (+/- 0.30) → logp-between=0.8,1.4		LogP: 1.1 (+/- 0.30) → logp-between=0.8,1.4
Line 47:		Line 47:
	As a ZINC query these constraints would be:		As a ZINC query these constraints would be:

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-tanimoto=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted-tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1>

	This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no		This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no

	<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-tanimoto=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1&count=50parallelize=no&distinct=no>		<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-unsorted-tanimoto-25=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1&count=50parallelize=no&distinct=no>

	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Teague Sterling: /* = More Examples */

2015-09-15T18:23:11Z

= More Examples

← Older revision		Revision as of 18:23, 15 September 2015
Line 11:		Line 11:
	http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1		http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1

	==~~= More~~ Examples ==		== Examples ==

	~~Getting decoys for Aspirin~~

			=== Getting decoys for Aspirin (ZINC000000000053) ===
	2D Decoys (need to generate DB2 files and compute charge yourself)		2D Decoys (need to generate DB2 files and compute charge yourself)
	Visualize:		Visualize: <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D?>
	<http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D?>		Download: <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100>

	Download:
	<http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100>

	3D Decoys (Can DOCK directly)		3D Decoys (Can DOCK directly)
	Visualize:		Visualize: <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D>
	<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D>		Download (SMILES & Explicit Charge): <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100>
			Download (DB2): <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100>
	Download (SMILES & Explicit Charge):
	<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100>

	Download (DB2):
	<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100>


	Allowed args:		Allowed args:
Line 37:		Line 27:
	* resolve: Look up zinc_ids if possible		* resolve: Look up zinc_ids if possible
	* unique: Only return unique decoys (if you POST with "for" as a file instead)		* unique: Only return unique decoys (if you POST with "for" as a file instead)


	You could also do decoys "by hand" to have more control:		You could also do decoys "by hand" to have more control:
	http://zinc15.docking.org/substances/?~ecfp4_fp-unsorted_tanimoto,.2=zinc55&mwt-between=270,330&logp-between=1.8,2.4&purchasability=for-sale		http://zinc15.docking.org/substances/?~ecfp4_fp-unsorted_tanimoto,.2=zinc55&mwt-between=270,330&logp-between=1.8,2.4&purchasability=for-sale

			=== Getting Decoys for a SMILES (e.g. not in ZINC) ===
			Getting Decoys for a SMILES string can be written as a general ZINC query on either the substances (2D) resource or the protomers resource (3D). Constraints can be added for further refinement.
			Currently you need to have a smiles string (e.g. `CN(C)C(=O)c1ccc(O)cc1`) as well as the physical properties you of that compound (i.e. molecular weight, logp, etc.). This requirement will soon be removed and replaced with a simple form.

			Molecular Properties (Criteria) → URL Parameters:

			SMILES: CN(C)C(=O)c1ccc(O)cc1 (ECFP4-tanimoto < 0.25) → ~substance.ecfp4_fp-tanimoto=CN(C)C(=O)c1ccc(O)cc1
			MWT: 165.2 (+/- 10%) → mwt-between=148.67,181.72
			LogP: 1.1 (+/- 0.30) → logp-between=0.8,1.4
			Donors: 1 (==) → hbd=1
			Acceptors: 2 (==) → hba=2
			Charge: 0 (==) → charge=0
			Rotatable Bonds: 1 (==) → rb=1

			As a ZINC query these constraints would be:

			<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-tanimoto=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1>

			This query can be made faster by requesting only 50 and adding a few additional execution rules: count=50&parallelize=no&distinct=no

			<http://zinc15.docking.org/protomers/?~substance.ecfp4_fp-tanimoto=CN(C)C(=O)c1ccc(O)cc1&mwt-between=148.67,181.72&logp-between=0.8,1.4&hbd=1&hba=2&charge=0&rb=1&count=50parallelize=no&distinct=no>

	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Teague Sterling at 17:13, 15 September 2015

2015-09-15T17:13:44Z

← Older revision		Revision as of 17:13, 15 September 2015
Line 11:		Line 11:
	http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1		http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1

	=== Examples		=== More Examples ==

	Getting decoys for Aspirin		Getting decoys for Aspirin
Line 17:		Line 17:
	2D Decoys (need to generate DB2 files and compute charge yourself)		2D Decoys (need to generate DB2 files and compute charge yourself)
	Visualize:		Visualize:
	zinc15.docking.org/substances/ZINC000000000053/decoys/2D		<http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D?>

	Download:		Download:
	zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100		<http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100>

	3D Decoys (Can DOCK directly)		3D Decoys (Can DOCK directly)
	Visualize:		Visualize:
	zinc15.docking.org/substances/ZINC000000000053/decoys/3D		<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D>

	Download (SMILES & Explicit Charge):		Download (SMILES & Explicit Charge):
	zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100		<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100>

	Download (DB2):		Download (DB2):
	zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100		<http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100>

Teague Sterling at 17:11, 15 September 2015

2015-09-15T17:11:34Z

← Older revision		Revision as of 17:11, 15 September 2015
Line 11:		Line 11:
	http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1		http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1

	== Examples		=== Examples

	Getting decoys for Aspirin		Getting decoys for Aspirin

Teague Sterling: Adding some example links

2015-09-15T17:11:10Z

Adding some example links

@@ Line 10: / Line 10: @@
   http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1
 Allowed args:
 * count: How many

Frodo: asff

2015-06-22T15:58:35Z

asff

← Older revision		Revision as of 15:58, 22 June 2015
Line 15:		Line 15:
	* unique: Only return unique decoys (if you POST with "for" as a file instead)		* unique: Only return unique decoys (if you POST with "for" as a file instead)


			You could also do decoys "by hand" to have more control:
			http://zinc15.docking.org/substances/?~ecfp4_fp-unsorted_tanimoto,.2=zinc55&mwt-between=270,330&logp-between=1.8,2.4&purchasability=for-sale

	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Frodo: asfd

2015-06-22T13:56:11Z

asfd

← Older revision		Revision as of 13:56, 22 June 2015
Line 4:		Line 4:

	If you want decoys for a molecule in ZINC, say 556, use		If you want decoys for a molecule in ZINC, say 556, use
	http://~~band~~.~~desktop.ucsf.bkslab~~.org~~:8088~~/substances/ZINC000000000556/decoys/3D.sdf		http://zinc15.docking.org/substances/ZINC000000000556/decoys/3D.sdf

			If you want decoys in 2D:
			http://zinc15.docking.org/substances/ZINC000019632927/decoys/2D/

			http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1
			Allowed args:
			* count: How many
			* resolve: Look up zinc_ids if possible
			* unique: Only return unique decoys (if you POST with "for" as a file instead)


	[[DUDE]] is a free directory of useful decoys for [[virtual screening]].		[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

Frodo: asdf

2015-06-11T05:02:46Z

asdf

← Older revision		Revision as of 05:02, 11 June 2015
Line 3:		Line 3:
	Decoys are important for judging the performance of [[molecular docking]] algorithms.		Decoys are important for judging the performance of [[molecular docking]] algorithms.

	~~The~~ [[~~DUD database~~]] is a free directory of useful decoys for [[virtual screening]].		If you want decoys for a molecule in ZINC, say 556, use
			http://band.desktop.ucsf.bkslab.org:8088/substances/ZINC000000000556/decoys/3D.sdf

			[[DUDE]] is a free directory of useful decoys for [[virtual screening]].

	For more information on preparation see		For more information on preparation see