Reactivity axis - Revision history

Frodo: /* The Reactivity Axis */ asdf

2018-03-24T19:45:41Z

The Reactivity Axis: asdf

← Older revision		Revision as of 19:45, 24 March 2018
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	\| A \|\| Anodyne aka no-PAINS \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| very unlikely to react or cause trouble in any way \|\| 0		\| A \|\| Anodyne aka no-PAINS \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| very unlikely to react or cause trouble in any way \|\| 0
	\|-		\|-
	\| B \|\| ~~Reserved1~~ \|\| ~~Future Use~~ \|\| ~~no matches~~ \|\| ~~not used, but future use might include~~ chromophores (assay interference), heptanes (entropy), quarts (not permeable), ~~even methyl and ethyl esters (may hydrolyze)~~ \|\| 5		\| B \|\| Chromophore \|\| little things people complain about: nitros, chromophores, hydroxamates \|\| not sure \|\| chromophores (assay interference), heptanes (entropy), quarts (not permeable), nitros, hydroxamates. last chance to complain before anodyne \|\| 5
	\|-		\|-
	\| C \|\| ZINC clean aka PAINS-ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| many PAINS are simply frequent hitters, and many legitimate bioactives include PAINS. you may well wish to screen them and use PAINS as an annotation, not a filter \|\| 10		\| C \|\| ZINC clean aka PAINS-ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| many PAINS are simply frequent hitters, and many legitimate bioactives include PAINS. you may well wish to screen them and use PAINS as an annotation, not a filter \|\| 10

Frodo: /* The Reactivity Axis */ asdf

2016-01-05T01:14:25Z

The Reactivity Axis: asdf

← Older revision		Revision as of 01:14, 5 January 2016
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	! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| internal score		! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| internal score
	\|-		\|-
	\| A \|\| Anodyne aka no-PAINS \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| ~~example~~ \|\| 0		\| A \|\| Anodyne aka no-PAINS \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| very unlikely to react or cause trouble in any way \|\| 0
	\|-		\|-
	\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| ~~example~~ \|\| 5		\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| not used, but future use might include chromophores (assay interference), heptanes (entropy), quarts (not permeable), even methyl and ethyl esters (may hydrolyze) \|\| 5
	\|-		\|-
	\| C \|\| ZINC clean aka PAINS-ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| ~~example~~ \|\| 10		\| C \|\| ZINC clean aka PAINS-ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| many PAINS are simply frequent hitters, and many legitimate bioactives include PAINS. you may well wish to screen them and use PAINS as an annotation, not a filter \|\| 10
	\|-		\|-
	\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20		\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20
	\|-		\|-
	\| E \|\| mildly reactive \|\| mildly electrophilic or nucleophilic group~~, including PAINS where these mechanisms have been assigned.~~ \|\| pattern_type_fk in (1,2) \|\| aldhydes, thiols, michael acceptors, epoxides \|\| 30		\| E \|\| mildly reactive \|\| mildly electrophilic, nucleophilic group or redox \|\| pattern_type_fk in (1,2) \|\| e.g. aldhydes, imines, thiols, michael acceptors, epoxides \|\| 30
	\|-		\|-
	\| F \|\| Reserved3 \|\| Future Use \|\| no matches \|\| example \|\| 40		\| F \|\| Reserved3 \|\| Future Use \|\| no matches \|\| example \|\| 40
	\|-		\|-
	\| G \|\| reactive \|\| electrophile or ~~nucleophile, including PAINS where these mechanisms have been assigned~~ \|\| pattern_type in (3,4) \|\| ~~alpha halo ketones, alkyl halides~~. ~~Note includes cancer drugs.~~ \|\| 50		\| G \|\| reactive \|\| generally electrophile, nucleophile or redox \|\| pattern_type in (3,4) \|\| e.g. thiocyanates, isothiocyanates \|\| 50
	\|-		\|-
	\| H \|\| Reserved4 \|\| Future use \|\| no matches \|\| example \|\| 60		\| H \|\| Reserved4 \|\| Future use \|\| no matches \|\| example \|\| 60
	\|-		\|-
	\| I \|\| ~~Unstable~~ \|\| ~~Highly~~ reactive \|\| pattern_origin=7 \|\| typically reagents~~, but~~ could be used for covalent binding. e.g. boronic acids \|\| 70		\| I \|\| Highly reactive \|\| Too reactive to be considered as non-covalent ligands \|\| pattern_origin=7 \|\| typically reagents; could be used for covalent binding. e.g. boronic acids. alpha halo ketones, alkyl halides. Note includes cancer drugs. \|\| 70
	\|}		\|}

Frodo: asdf

2015-09-08T22:42:40Z

asdf

← Older revision		Revision as of 22:42, 8 September 2015
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	Here we describe the reactivity axis in the ZINC15, particularly in the exported subsets available via the [[tranche browser]].		Here we describe the reactivity axis in the ZINC15, particularly in the exported subsets available via the [[tranche browser]].

	In the discussion below, ZINC12 standard subsets included: A~~, B~~, C~~, D~~, E.		In the discussion below, ZINC12 standard subsets included: A, C, E.

	The ZINC12 subsets known as "clean" subsets were just A~~, B,~~ C, D.		The ZINC12 subsets known as "clean" subsets were just A and C.

			The "I" subset was not loaded in ZINC12, and is only available in 2D (and possibly covalent libraries)

	== The Reactivity Axis ==		== The Reactivity Axis ==

Frodo: asdf

2015-09-08T22:41:40Z

asdf

← Older revision		Revision as of 22:41, 8 September 2015
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	we need to classify pains by assumed mechanism		we need to classify pains by assumed mechanism

	~~397 pains never hit any compound in zinc~~


	[[Category:ZINC15]]		[[Category:ZINC15]]
	[[Category:PAINS]]		[[Category:PAINS]]

Frodo: asdf

2015-09-08T22:37:03Z

asdf

← Older revision		Revision as of 22:37, 8 September 2015
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	! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| internal score		! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| internal score
	\|-		\|-
	\| A \|\| Anodyne \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| example \|\| 0		\| A \|\| Anodyne aka no-PAINS \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| example \|\| 0
	\|-		\|-
	\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5		\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5

Frodo: asdf

2015-09-08T22:36:31Z

asdf

← Older revision		Revision as of 22:36, 8 September 2015
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	\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5		\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5
	\|-		\|-
	\| C \|\| PAINS ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| example \|\| 10		\| C \|\| ZINC clean aka PAINS-ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| example \|\| 10
	\|-		\|-
	\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20		\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20

Frodo: /* The Reactivity Axis */ asdf

2015-09-03T19:44:41Z

The Reactivity Axis: asdf

← Older revision		Revision as of 19:44, 3 September 2015
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	\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5		\| B \|\| Reserved1 \|\| Future Use \|\| no matches \|\| example \|\| 5
	\|-		\|-
	\| C \|\| PAINS ~~sans mechanism~~ \|\| Worst problem is, PAINS ~~without a~~ clear mechanism ~~matches~~ \|\| pattern_origin_fk =2 \|\| example \|\| 10		\| C \|\| PAINS ok \|\| Worst problem is a match with a PAINS with not clear mechanism \|\| pattern_origin_fk =2 \|\| example \|\| 10
	\|-		\|-
	\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20		\| D \|\| Reserved2 \|\| Future Use \|\| no matches \|\| example \|\| 20

Frodo: asdf

2015-08-27T15:50:51Z

asdf

← Older revision		Revision as of 15:50, 27 August 2015
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	Here we describe the ~~"clean"~~ axis in the exported subsets ~~of ZINC15~~.		Here we describe the reactivity axis in the ZINC15, particularly in the exported subsets available via the [[tranche browser]].

	~~Traditionally~~, ~~ZINC~~ standard subsets included: A, B, C, D, E.		In the discussion below, ZINC12 standard subsets included: A, B, C, D, E.

	~~ZINC~~ "clean" subsets were just A, B, C, D.		The ZINC12 subsets known as "clean" subsets were just A, B, C, D.

	== The ~~Clean~~ Axis ==		== The Reactivity Axis ==
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-

Frodo: Frodo moved page Clean axis to Reactivity axis: we now use reactivity instead of clean

2015-08-27T15:48:51Z

Frodo moved page Clean axis to Reactivity axis: we now use reactivity instead of clean

← Older revision	Revision as of 15:48, 27 August 2015
(No difference)

Frodo: /* The Clean Axis */ sdaf

2015-08-13T04:18:32Z

The Clean Axis: sdaf

← Older revision		Revision as of 04:18, 13 August 2015
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| score		! Class !! Nickname !! Description \|\| How computed \|\| Examples \|\| internal score
	\|-		\|-
	\| A \|\| Anodyne \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| example \|\| 0		\| A \|\| Anodyne \|\| No flags of any kind set \|\| pattern_origin_fk is null \|\| example \|\| 0