Category:SEA - Revision history

Khtang: /* Target vs Targets */

2022-07-25T23:03:21Z

Target vs Targets

← Older revision		Revision as of 23:03, 25 July 2022
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	=== Target vs Targets ===		=== Target vs Targets ===
	==== Target vs Target ====		==== Target vs Target ====
	[[File:target_vs_target.png\|~~500px~~\|right\|alt text]]		[[File:target_vs_target.png\|700px\|right\|alt text]]
	* The user wants to compare the ligand similarity between two targets		* The user wants to compare the ligand similarity between two targets
	* The user inputs the target id one as the reference target and one as the query target(<b>/search</b> route)		* The user inputs the target id one as the reference target and one as the query target(<b>/search</b> route)

Khtang: /* Target vs Targets */

2022-07-25T23:02:58Z

Target vs Targets

← Older revision		Revision as of 23:02, 25 July 2022
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	=== Target vs Targets ===		=== Target vs Targets ===
	==== Target vs Target ====		==== Target vs Target ====
			[[File:target_vs_target.png\|500px\|right\|alt text]]
	* The user wants to compare the ligand similarity between two targets		* The user wants to compare the ligand similarity between two targets
	* The user inputs the target id one as the reference target and one as the query target(<b>/search</b> route)		* The user inputs the target id one as the reference target and one as the query target(<b>/search</b> route)

Khtang: /* Compounds vs Targets */

2022-07-25T23:01:59Z

Compounds vs Targets

← Older revision		Revision as of 23:01, 25 July 2022
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	==== Compounds vs Library screen ====		==== Compounds vs Library screen ====
			[[File:compound_vs_target.png\|300px\|right\|alt text]]
	* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)		* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)
	~~[[File:compound_vs_target.png\|300px\|right\|alt text]]~~

	==== Compound(s) vs Specified Library targets ====		==== Compound(s) vs Specified Library targets ====
	* Same as above except instead of returning results for all targets in the library, just return results for the requested targets		* Same as above except instead of returning results for all targets in the library, just return results for the requested targets

Khtang: /* Compounds vs Library screen */

2022-07-25T23:01:38Z

Compounds vs Library screen

← Older revision		Revision as of 23:01, 25 July 2022
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	==== Compounds vs Library screen ====		==== Compounds vs Library screen ====
	* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)		* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)
	[[File:compound_vs_target.png\|~~700px~~\|right\|alt text]]		[[File:compound_vs_target.png\|300px\|right\|alt text]]

	==== Compound(s) vs Specified Library targets ====		==== Compound(s) vs Specified Library targets ====

Khtang: /* Compounds vs Library screen */

2022-07-25T23:01:13Z

Compounds vs Library screen

← Older revision		Revision as of 23:01, 25 July 2022
Line 33:		Line 33:
	==== Compounds vs Library screen ====		==== Compounds vs Library screen ====
	* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)		* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)
			[[File:compound_vs_target.png\|700px\|right\|alt text]]

	==== Compound(s) vs Specified Library targets ====		==== Compound(s) vs Specified Library targets ====
	* Same as above except instead of returning results for all targets in the library, just return results for the requested targets		* Same as above except instead of returning results for all targets in the library, just return results for the requested targets

Khtang: /* Compound vs Library screen */

2022-07-25T22:57:20Z

Compound vs Library screen

← Older revision		Revision as of 22:57, 25 July 2022
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	=== Compounds vs Targets ===		=== Compounds vs Targets ===
	==== Compound vs Library screen ====		==== Compound vs Library screen ====
	[[File:compound_vs_library.png\|~~500px~~\|right\|alt text]]		[[File:compound_vs_library.png\|700px\|right\|alt text]]
	* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.		* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.
	* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)		* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)

Khtang: /* Compound vs Library screen */

2022-07-25T22:56:56Z

Compound vs Library screen

← Older revision		Revision as of 22:56, 25 July 2022
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	=== Compounds vs Targets ===		=== Compounds vs Targets ===
	==== Compound vs Library screen ====		==== Compound vs Library screen ====
	[[File:compound_vs_library.png\|~~left~~\|alt text]]		[[File:compound_vs_library.png\|500px\|right\|alt text]]
	* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.		* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.
	* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)		* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)
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	** Similar targets to predicted target (feature request)		** Similar targets to predicted target (feature request)
	** Sequence similarity and ligand similarity trees for predicted targets (feature request)		** Sequence similarity and ligand similarity trees for predicted targets (feature request)

	==== Compounds vs Library screen ====		==== Compounds vs Library screen ====
	* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)		* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)

Khtang: /* Compounds vs Targets */

2022-07-25T22:56:36Z

Compounds vs Targets

← Older revision		Revision as of 22:56, 25 July 2022
Line 21:		Line 21:
	=== Compounds vs Targets ===		=== Compounds vs Targets ===
	==== Compound vs Library screen ====		==== Compound vs Library screen ====
			[[File:compound_vs_library.png\|left\|alt text]]
	* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.		* User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.
	* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)		* The user inputs the smiles and optionally compound IDs and selects a library (e.g. ChEMBL27 by protein) (<b>/search</b> route)
Line 29:		Line 30:
	** Similar targets to predicted target (feature request)		** Similar targets to predicted target (feature request)
	** Sequence similarity and ligand similarity trees for predicted targets (feature request)		** Sequence similarity and ligand similarity trees for predicted targets (feature request)

	==== Compounds vs Library screen ====		==== Compounds vs Library screen ====
	* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)		* Same as above except instead of going directly to <b>/compound_vs_target route</b>, go to a summary page for each compound (<b>/results</b> route)

Khtang: /* Using the SEA website */

2022-07-25T22:27:09Z

Using the SEA website

@@ Line 18: / Line 18: @@
 == Publications ==
-== Using the SEA website ==
+== Use cases ==
 == Obtaining a private copy of SEA ==

Khtang: /* Citing SEA */

2019-01-03T23:12:30Z

Citing SEA

← Older revision		Revision as of 23:12, 3 January 2019
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	'''SEA''' relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps. It is provided by the [[Shoichet Laboratory]] in the [[Department of Pharmaceutical Chemistry]] at the University of California, San Francisco ([[UCSF]]).		'''SEA''' relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps. It is provided by the [[Shoichet Laboratory]] in the [[Department of Pharmaceutical Chemistry]] at the University of California, San Francisco ([[UCSF]]).
	== Citing SEA ==		== Citing SEA ==
	To cite SEA, please reference Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007).<ref>[http://dx.doi.org/10.1038/nbt1284 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007)]</ref>		To cite SEA, please reference Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007)<ref>[http://dx.doi.org/10.1038/nbt1284 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007)]</ref>.

	== Publications ==		== Publications ==