Aggregator Advisor - Revision history

Khtang: /* Query procedure */

2019-01-03T22:35:03Z

Query procedure

← Older revision		Revision as of 22:35, 3 January 2019
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	== Query procedure ==		== Query procedure ==

	For a query molecule(submitted through the web-interface):		For a query molecule(submitted through the web-interface):
	Look up molecule		===1. Look up molecule===

	If (aggregator) then		If (aggregator) then
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	endif		endif

	~~compute~~ similarity to aggregators, ambiguous,		===2. Compute similarity to aggregators, ambiguous,===

	If (similar to aggregator) then		If (similar to aggregator) then
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	endif		endif

	~~compute~~ murcko scaffold.		===3. Compute murcko scaffold.===
	check similarity of murcko scaffold vs aggregators, ambiguous		check similarity of murcko scaffold vs aggregators, ambiguous

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	endif		endif

	~~compute~~ physical properties.		===4. Compute physical properties.===
	if logP > 3.5, say: warning		if logP > 3.5, say: warning
	else		else

Khtang at 22:31, 3 January 2019

2019-01-03T22:31:34Z

← Older revision		Revision as of 22:31, 3 January 2019
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	The next layer is the web-service, which allows to query the AggregatorAdvisor. The Front-end uses the aggregate advisor web-service the same way as any third-party would use it.		The next layer is the web-service, which allows to query the AggregatorAdvisor. The Front-end uses the aggregate advisor web-service the same way as any third-party would use it.
	The users of the system make XML-RPC requests and receive the query responses in XML-RPC format. The protocol of operation is given in the section *[[Web Services Description]]		The users of the system make XML-RPC requests and receive the query responses in XML-RPC format. The protocol of operation is given in the section *[[Web Services Description]]



	*[[Interacting with Chemaxon dataset]]		*[[Interacting with Chemaxon dataset]]
			==References==
			<references />


	[[Category:Services]]		[[Category:Services]]

Khtang at 22:30, 3 January 2019

2019-01-03T22:30:56Z

← Older revision		Revision as of 22:30, 3 January 2019
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			==About==
	Aggregator advisor is a service to predict aggregation based on similarity to know aggregators, and calculated LogP.		Aggregator advisor is a service to predict aggregation based on similarity to know aggregators, and calculated LogP.

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	Aggregator Advisor is a system for finding similar molecules to the query that are known aggregators or non-aggregators. The heart of the system is the Chemaxon molecular query system. The Aggregate Advisor is a wrapper around the chaemaxon library. The operation sequence of Aggregate Advisor is following		Aggregator Advisor is a system for finding similar molecules to the query that are known aggregators or non-aggregators. The heart of the system is the Chemaxon molecular query system. The Aggregate Advisor is a wrapper around the chaemaxon library. The operation sequence of Aggregate Advisor is following

			==Cite Aggregator Advisor==
			To cite Aggregator Advisor, please use: Irwin, Duan, Torosyan, Doak, Ziebart, Sterling, Tumanian and Shoichet, J Med Chem, 2015, 58(1 7), 7076-7087<ref>[http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b01105 Irwin, Duan, Torosyan, Doak, Ziebart, Sterling, Tumanian and Shoichet, J Med Chem, 2015, 58(1 7), 7076-7087]</ref>.

	== Query procedure ==		== Query procedure ==

Khtang: /* System design */

2018-12-28T21:53:56Z

System design

← Older revision		Revision as of 21:53, 28 December 2018
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	The Aggregate Advisor application consists of several software layers. each layer wraps around the lower one.		The Aggregate Advisor application consists of several software layers. each layer wraps around the lower one.
	The top layer is the UI engine, which allows a user of the system to draw and submit a query molecule and view the results in a formatted form, together with the structural image of the response molecules. Additionally the user of te system can browse the library of known aggregators. This level is built in PHP using ~~CodeIgniter(~~http://codeigniter.com/~~)library~~. For drawing capability it uses		The top layer is the UI engine, which allows a user of the system to draw and submit a query molecule and view the results in a formatted form, together with the structural image of the response molecules. Additionally the user of te system can browse the library of known aggregators. This level is built in PHP using [http://codeigniter.com/ CodeIgniter Library]. For drawing capability it uses
	the WebME editor. Adittionally it requests the SEA rendering system for displaying the images of the molecules.		the WebME editor. Adittionally it requests the SEA rendering system for displaying the images of the molecules.

Frodo at 00:55, 11 March 2014

2014-03-11T00:55:58Z

← Older revision		Revision as of 00:55, 11 March 2014
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	* [http://advisor.docking.org advisor.docking.org]		* [http://advisor.docking.org advisor.docking.org]

	~~[[Category:Websites]]~~
	~~[[Category:Services]]~~


	Aggregator Advisor is a system for finding similar molecules to the query that are known aggregators or non-aggregators. The heart of the system is the Chemaxon molecular query system. The Aggregate Advisor is a wrapper around the chaemaxon library. The operation sequence of Aggregate Advisor is following		Aggregator Advisor is a system for finding similar molecules to the query that are known aggregators or non-aggregators. The heart of the system is the Chemaxon molecular query system. The Aggregate Advisor is a wrapper around the chaemaxon library. The operation sequence of Aggregate Advisor is following
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	*[[Interacting with Chemaxon dataset]]		*[[Interacting with Chemaxon dataset]]


			[[Category:Services]]

Therese: 6 revisions

2012-10-08T18:10:25Z

6 revisions

← Older revision

Revision as of 18:10, 8 October 2012

Frodo at 01:20, 11 March 2012

2012-03-11T01:20:37Z

New page

Aggregator advisor is a service to predict aggregation based on similarity to know aggregators, and calculated LogP.

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

[[Category:Websites]]
[[Category:Services]]

Aggregator Advisor is a system for finding similar molecules to the query that are known aggregators or non-aggregators. The heart of the system is the Chemaxon molecular query system. The Aggregate Advisor is a wrapper around the chaemaxon library. The operation sequence of Aggregate Advisor is following

== Query procedure ==

For a query molecule(submitted through the web-interface):
Look up molecule

If (aggregator) then
say so. give literature reference (justification)
stop
else (ambiguous) then
say so. give literature reference (justification)
stop
else (non-aggregator) then
say so. give literature reference (justification)
continue
endif

compute similarity to aggregators, ambiguous,

If (similar to aggregator) then
say so. give literature reference (justification),
similar molecule and similarity level
stop
else (similar to ambiguous) then
say so. give literature reference (justification)
similar molecule and similarity level
endif

compute murcko scaffold.
check similarity of murcko scaffold vs aggregators, ambiguous

If (murcko is substructure of aggregator) th
say so. give literature reference (justification)
show database molecule we are a substructure of
stop
else (murcko is substructure of ambiguous) then
say so. give literature reference (justification)
show database molecule we are a substructure of
endif

compute physical properties.
if logP > 3.5, say: warning
else
For now, say: no reason to suspect this is an aggregators.

==System design==

The Aggregate Advisor application consists of several software layers. each layer wraps around the lower one.
The top layer is the UI engine, which allows a user of the system to draw and submit a query molecule and view the results in a formatted form, together with the structural image of the response molecules. Additionally the user of te system can browse the library of known aggregators. This level is built in PHP using CodeIgniter(http://codeigniter.com/)library. For drawing capability it uses
the WebME editor. Adittionally it requests the SEA rendering system for displaying the images of the molecules.

The next layer is the web-service, which allows to query the AggregatorAdvisor. The Front-end uses the aggregate advisor web-service the same way as any third-party would use it.
The users of the system make XML-RPC requests and receive the query responses in XML-RPC format. The protocol of operation is given in the section *[[Web Services Description]]

*[[Interacting with Chemaxon dataset]]