Hit picking party - Revision history

Sevigneron: /* Before the party */

2024-06-06T17:10:28Z

Before the party

← Older revision		Revision as of 17:10, 6 June 2024
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	= Before the party =		= Before the party =
	The investigator who performed the virtual screen looks critically at the results, selecting perhaps a dozen or two interesting compounds from among the top 500. Several copies of the top 500 list are printed, sometimes with additional supporting documentation, and distributed to the participants. Check [[CSD]] data for compound pose information. The [[Pka\|pKa]] of each molecule can be checked. Think about [[reactive groups]] for molecules. Think about PAINS http://pasilla.health.unm.edu/tomcat/biocomp/smartsfilter		The investigator who performed the virtual screen looks critically at the results, selecting perhaps a dozen or two interesting compounds from among the top 500. Several copies of the top 500 list are printed, sometimes with additional supporting documentation, and distributed to the participants. Check [[CSD]] data for compound pose information. The [[Pka\|pKa]] of each molecule can be checked. Think about specific ligand-protein interactions (A Medicinal Chemist’s Guide to Molecular Interactions, J. Med. Chem. 2010, 53, 5061–5084 DOI: 10.1021/jm100112j, can be a nice resource for thinking of what to look for). Think about [[reactive groups]] for molecules. Think about PAINS http://pasilla.health.unm.edu/tomcat/biocomp/smartsfilter

	= During the party =		= During the party =

Frodo: asdf

2024-06-01T00:21:41Z

asdf

← Older revision		Revision as of 00:21, 1 June 2024
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	[[Category:Tutorials]]		[[Category:Tutorials]]
	[[Category:Docking]]		[[Category:Docking]]
			[[Category:Narratives]]

Frodo at 09:15, 13 March 2014

2014-03-13T09:15:23Z

← Older revision		Revision as of 09:15, 13 March 2014
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	Before we buy compounds, we have a hit picking party.		Before we buy compounds, we have a hit picking party.

			{{TOCright}}

	= Before the party =		= Before the party =

Frodo at 23:34, 11 March 2014

2014-03-11T23:34:44Z

← Older revision		Revision as of 23:34, 11 March 2014
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	Before we buy compounds, we have a hit picking party.		Before we buy compounds, we have a hit picking party.

	** this document is still in progress.


	= Before the party =		= Before the party =
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	= Epilogue =		= Epilogue =
	Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.docking.org/]		Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.docking.org/]


	~~-- John Irwin~~


	[[Category:Tutorials]]		[[Category:Tutorials]]
			[[Category:Docking]]

Therese: 15 revisions

2012-10-08T20:25:29Z

15 revisions

← Older revision

Revision as of 20:25, 8 October 2012

Rgc: added Nir's PAINS link

2012-07-07T05:40:51Z

added Nir's PAINS link

← Older revision		Revision as of 05:40, 7 July 2012
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	= Before the party =		= Before the party =
	The investigator who performed the virtual screen looks critically at the results, selecting perhaps a dozen or two interesting compounds from among the top 500. Several copies of the top 500 list are printed, sometimes with additional supporting documentation, and distributed to the participants. Check [[CSD]] data for compound pose information. The [[Pka\|pKa]] of each molecule can be checked. Think about [[reactive groups]] for molecules.		The investigator who performed the virtual screen looks critically at the results, selecting perhaps a dozen or two interesting compounds from among the top 500. Several copies of the top 500 list are printed, sometimes with additional supporting documentation, and distributed to the participants. Check [[CSD]] data for compound pose information. The [[Pka\|pKa]] of each molecule can be checked. Think about [[reactive groups]] for molecules. Think about PAINS http://pasilla.health.unm.edu/tomcat/biocomp/smartsfilter

	= During the party =		= During the party =

Frodo: /* During the party */

2011-11-03T20:07:24Z

During the party

← Older revision		Revision as of 20:07, 3 November 2011
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	We take a good look at the site, and any crystallographic ligands or known experimental ligands. Think about enthalpic and entropic contributions to the binding. Think about possible water structure. Think of receptor flexibility, especially His, Gln, Asn, Ser, Tyr, Thr. Look for charged residues. Look at the surface colored by charge to look for greasy patches.		We take a good look at the site, and any crystallographic ligands or known experimental ligands. Think about enthalpic and entropic contributions to the binding. Think about possible water structure. Think of receptor flexibility, especially His, Gln, Asn, Ser, Tyr, Thr. Look for charged residues. Look at the surface colored by charge to look for greasy patches.

	Look at one ligand at a time, and rate each compound (e.g. 1, 2, or 3 checkmarks). People speak out, making favorable and unfavorable comments about each ligand. Broken molecules are rapidly ignored.		Look at one ligand at a time, and rate each compound (e.g. 1, 2, or 3 checkmarks). People speak out, making favorable and unfavorable comments about each ligand. Broken molecules are rapidly ignored.

			Watch out for very high or very low calculated LogP. Watch for weird conformations and weird protonation states and weird tautomeric forms. ZINC is imperfect, use your judgement. Watch out for super floppy molecules. Watch out for buried polarity or missed opportunities. hydroxide is the worst. If hydroxide ain't happy ain't nobody happy.

	= After the party =		= After the party =

Frodo: /* Epilogue */

2011-11-03T20:05:21Z

Epilogue

← Older revision		Revision as of 20:05, 3 November 2011
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	= Epilogue =		= Epilogue =
	Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.~~bkslab~~.org/]		Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.docking.org/]

Frodo: /* Epilogue */

2011-11-03T20:03:44Z

Epilogue

← Older revision		Revision as of 20:03, 3 November 2011
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	= Epilogue =		= Epilogue =
	Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.~~docking~~.org/]		Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.bkslab.org/]

Frodo: /* Epilogue */

2011-11-03T20:03:22Z

Epilogue

← Older revision		Revision as of 20:03, 3 November 2011
Line 16:		Line 16:

	= Epilogue =		= Epilogue =
	Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands.		Sometimes we go through several iterations. If no hits arise, we go back to the drawing board. We try to incorporate all available information, both in the modeling, and in the judgement of the ligands. Watch out for aggregators, and be sure to control for these during the experiments. [http://advisor.docking.org/]