Chemistry Commons - Revision history

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	https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00754		https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00754
	https://github.com/Laboratoire-de-Chemoinformatique/SynthI		https://github.com/Laboratoire-de-Chemoinformatique/SynthI
			https://pubmed.ncbi.nlm.nih.gov/39868130/
			https://pubmed.ncbi.nlm.nih.gov/36171289/

	Research Groups		Research Groups
	/mnt/nfs/exi/zinc22/commons/research_groups		/mnt/nfs/exi/zinc22/commons/research_groups


	== Naming conventions ==		== Naming conventions ==

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	* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds		* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
	* Libraries in 2D and 3D are prepared and made available.		* Libraries in 2D and 3D are prepared and made available.
	* Biologists (and the computational chemists they collaborate with) search these databases for molecules that look interesting		* Biologists (and the computational chemists they collaborate with) search these databases via the Chemistry Commons for molecules that look interesting
	* A collaborative agreement or other understanding is reached between the synthetic chemist and the biology lab which can test the compounds		* A collaborative agreement or other understanding is reached between the synthetic chemist and the biology lab which can test the compounds
	* Compounds are prioritized for synthesis collaboratively between the chemists and the biologists		* Compounds are prioritized for synthesis collaboratively between the chemists and the biologists

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	== Outline ==		== Outline ==

	* Synthetic organic chemists wish to ~~discovery~~ relevance of their chemistry to biological problems		* Synthetic organic chemists wish to discover the relevance of their new chemistry to biological problems
	* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds		* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
	* Libraries in 2D and 3D are prepared and made available.		* Libraries in 2D and 3D are prepared and made available.

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	* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds		* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
	* Libraries in 2D and 3D are prepared and made available.		* Libraries in 2D and 3D are prepared and made available.
	* Biologists (and the computational chemists they ~~work~~ with) search these databases for molecules that look interesting		* Biologists (and the computational chemists they collaborate with) search these databases for molecules that look interesting
	* Compounds are prioritized for synthesis		* A collaborative agreement or other understanding is reached between the synthetic chemist and the biology lab which can test the compounds
	* A collaborative agreement is reached between the synthetic chemist and the biology lab ~~testing~~ the compounds		* Compounds are prioritized for synthesis collaboratively between the chemists and the biologists
	* Compounds are ~~produced,~~ tested~~, and, ideally~~, some compounds will work.		* Compounds are synthesized and then tested in the lab. Ideally, some compounds will work.
			* Potentially iterate to optimize for affinity and other properties.
			* Ideally, write paper, grant, patent, etc.
			* ...
			* Profit (including helping people)

	== How to get started ==		== How to get started ==

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	== Outline ==		== Outline ==

	* Synthetic organic chemists wish to ~~make~~ their chemistry ~~relevant~~ to ~~biology~~		* Synthetic organic chemists wish to discovery relevance of their chemistry to biological problems
	* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds		* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
	* Libraries in 2D and 3D are prepared and made available.		* Libraries in 2D and 3D are prepared and made available.
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	* Compounds are prioritized for synthesis		* Compounds are prioritized for synthesis
	* A collaborative agreement is reached between the synthetic chemist and the biology lab testing the compounds		* A collaborative agreement is reached between the synthetic chemist and the biology lab testing the compounds
	* Compounds are produced, tested, and, ideally, some compounds will work.		* Compounds are produced, tested, and, ideally, some compounds will work.

	== How to get started ==		== How to get started ==

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	* synthetic organic chemists who have developed new reaction schemes and wonder whether they make useful compounds		* synthetic organic chemists who have developed new reaction schemes and wonder whether they make useful compounds
	* biologists and medicinal chemists seeking new reagents for biology and always looking for new compounds		* biologists and medicinal chemists seeking new reagents for biology and always looking for new compounds
	* ~~as well as~~ computational chemists, who can assist both camps.		* computational chemists, who can assist both camps.

	== Outline ==		== Outline ==

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	The Chemistry Commons is ~~an effort~~ to ~~facilitate the connections between~~		The Chemistry Commons is a platform to connect investigators with mutual interests in ligand discovery.
	* synthetic organic chemists who have developed new reaction schemes		* synthetic organic chemists who have developed new reaction schemes and wonder whether they make useful compounds
	* biologists seeking new reagents for biology		* biologists and medicinal chemists seeking new reagents for biology and always looking for new compounds
	* as well as ~~medicinal chemists and~~ computational chemists.		* as well as computational chemists, who can assist both camps.

	== Outline ==		== Outline ==

Frodo: Frodo moved page Chemistry commons to Chemistry Commons without leaving a redirect: standardization

2024-05-24T20:06:17Z

Frodo moved page Chemistry commons to Chemistry Commons without leaving a redirect: standardization

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	The Chemistry Commons is an effort to facilitate the connections between		The Chemistry Commons is an effort to facilitate the connections between
	* synthetic organic chemists		* synthetic organic chemists who have developed new reaction schemes
	* biologists seeking new reagents for biology		* biologists seeking new reagents for biology
	* as well as medicinal chemists and computational chemists.		* as well as medicinal chemists and computational chemists.
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	== Outline ==		== Outline ==

	* Synthetic organic chemists ~~looking~~ to make their chemistry ~~available~~ to ~~explore.~~		* Synthetic organic chemists wish to make their chemistry relevant to biology
	* Chemists use the ~~chemistry commons~~ to articulate and enumerate libraries of accessible compounds		* Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
	* ~~With our assistance, libraries~~ in 2D and 3D are prepared and made available.		* Libraries in 2D and 3D are prepared and made available.
	* ~~Medicinal~~ chemists ~~and biologists seeking new chemistry for their biological targets use our tools to~~ search~~, download, and dock~~ these ~~libraries~~		* Biologists (and the computational chemists they work with) search these databases for molecules that look interesting
	* Compounds are prioritized for synthesis~~, and an~~ agreement is ~~made~~ between the synthetic chemist and the biology lab testing the compounds		* Compounds are prioritized for synthesis
	* ~~Ideally, compounds~~ are produced, tested, and, ideally, some compounds will work.		* A collaborative agreement is reached between the synthetic chemist and the biology lab testing the compounds
			* Compounds are produced, tested, and, ideally, some compounds will work.

	== How to get started ==		== How to get started ==
	If you are a synthetic organic chemist, with a new reaction scheme, please use our tools to define your reaction. [[CC:Library preparation]]		If you are a synthetic organic chemist, with a new reaction scheme, please use our tools to define your reaction. [[CC:Library preparation]]

	If you are a biologist or medicinal chemist, seeking new compounds for your target, ~~you can~~ search the libraries in 2D using Smallworld [[CC:Smallworld]] and Arthor [[CC:Arthor]] or in 3D using docking or other 3D methods. [[CC:Docking]]		If you are a biologist or medicinal chemist, seeking new compounds for your target, search the libraries in 2D using Smallworld [[CC:Smallworld]] and Arthor [[CC:Arthor]] or in 3D using docking or other 3D methods. [[CC:Docking]]

	If you would like to participate in the ~~chemistry commons~~, but are not quite sure how to get started, please reach out to chemistry4biology at gmail dot com.		If you would like to participate in the Chemistry Commons, but are not quite sure how to get started, please reach out to chemistry4biology at gmail dot com or join us for [[Weekly office hours]]


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	== Naming conventions ==		== Naming conventions ==
	ZINC-22 molecules have the form ~~ZINCnprxnnnnnnnn~~ where		ZINC-22 molecules have the form ZINCnprx01234567 where
	* n indicates the heavy atom count of the molecule		* n indicates the heavy atom count of the molecule
	* p indicates the calculated logP of the molecule		* p indicates the calculated logP bin of the molecule
	* r indicates the research group that ~~orginated~~ the reaction scheme		* r indicates the research group that originated the reaction scheme
	* x indicates the ordinal number of the reaction scheme from that research group		* x indicates the ordinal number of the reaction scheme from that research group
	* n is the ordinal for each molecule in this space.		* 01234567 is the ordinal for each molecule in this space (monotonic increasing from 1)
	* numbers are in radix-62, thus [0-9][a-z][A-Z]		* numbers are in radix-62, thus [0-9][a-z][A-Z]

	Synthetic organic research groups may ~~or may not actually do~~ the synthesis.		Synthetic organic research groups may elect to perform the synthesis, or to enable it to be performed by a third party.

	== Notes for Chemistry Commons developers ==		== Notes for Chemistry Commons developers ==

Khtang at 19:18, 20 September 2023

2023-09-20T19:18:39Z

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	Synthetic organic research groups may or may not actually do the synthesis.		Synthetic organic research groups may or may not actually do the synthesis.

			== Notes for Chemistry Commons developers ==



	[[Category:Commons]]		[[Category:Commons]]