Chemistry Commons: Difference between revisions
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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. | ||
| Line 6: | Line 6: | ||
== Outline == | == Outline == | ||
* Synthetic organic chemists | * Synthetic organic chemists wish to make their chemistry relevant to biology | ||
* Chemists use the | * Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds | ||
* | * 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 | ||
* 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 | ||
* 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, | 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 | 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]] | ||
| Line 30: | Line 31: | ||
== Naming conventions == | == Naming conventions == | ||
ZINC-22 molecules have the form | 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 | * 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 | ||
* | * 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 | 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 == | ||
Revision as of 21:16, 23 May 2024
The Chemistry Commons is an effort to facilitate the connections between
- synthetic organic chemists who have developed new reaction schemes
- biologists seeking new reagents for biology
- as well as medicinal chemists and computational chemists.
Outline
- Synthetic organic chemists wish to make their chemistry relevant to biology
- Chemists use the Chemistry Commons to articulate and enumerate libraries of accessible compounds
- 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
- Compounds are prioritized for synthesis
- 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
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, 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 or join us for Weekly office hours
Literature references
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00754 https://github.com/Laboratoire-de-Chemoinformatique/SynthI
Research Groups
/mnt/nfs/exi/zinc22/commons/research_groups
Naming conventions
ZINC-22 molecules have the form ZINCnprx01234567 where
- n indicates the heavy atom count of the molecule
- p indicates the calculated logP bin of the molecule
- r indicates the research group that originated the reaction scheme
- x indicates the ordinal number of the reaction scheme from that research group
- 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]
Synthetic organic research groups may elect to perform the synthesis, or to enable it to be performed by a third party.