Chemistry Commons: Difference between revisions
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The Chemistry Commons is | The Chemistry Commons is a platform to connect investigators with mutual interests in ligand discovery. | ||
* synthetic organic chemists | * 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 | ||
* | * computational chemists, who can assist both camps. | ||
== Outline == | == Outline == | ||
* Synthetic organic chemists | * Synthetic organic chemists wish to discover the relevance of their new chemistry to biological problems | ||
* 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 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 | ||
* Ideally, compounds | * Compounds are prioritized for synthesis collaboratively between the chemists and the biologists | ||
* 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 == | ||
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]] | ||
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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 == | ||
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 == | |||
[[Category:Commons]] | [[Category:Commons]] | ||
Latest revision as of 19:52, 21 February 2025
The Chemistry Commons is a platform to connect investigators with mutual interests in ligand discovery.
- 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
- computational chemists, who can assist both camps.
Outline
- 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
- Libraries in 2D and 3D are prepared and made available.
- 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
- Compounds are prioritized for synthesis collaboratively between the chemists and the biologists
- 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
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 https://pubmed.ncbi.nlm.nih.gov/39868130/ https://pubmed.ncbi.nlm.nih.gov/36171289/
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.