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Tag: cheminformatics

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog

TMAP on Apple Silicon

16 April 202422 April 2024 chris

tmap is a very fast visualisation library for large, high-dimensional data sets. It was published in 2020 DOI and the code is available on GitHub

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog

A Jupyter Notebook to compare similarity between molecules

11 April 202411 April 2024 chris

I’m sometimes asked for a tool to compare the similarity of a list of molecules with every other molecule in the list. I suspect there

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Data Analysis Tools Jupyter Notebook Macinchem Blog

Project Jupyter wins Technical Advancement to Enable Open Science Award

23 March 202423 March 2024 chris

Project Jupyter is the winner of the White House OSTP “Technical Advancement to Enable Open Science” category. Open science relies on technical advancements and infrastructures

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Macinchem Blog Science Apps

ChemDoodle Web Components v10 is Available

21 March 202421 March 2024 chris

This is a feature update (v10.0) to the ChemDoodle Web Components library. Additions

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Macinchem Blog Science Apps

Rowan improves security.

15 March 202415 March 2024 chris

The latest Rowan newsletter highlights security. https://rowansci.substack.com/p/taking-security-seriously In particular, they have improved the internal security to protect data in submitted jobs. You can read more

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Macinchem Blog Science Apps

Rowan calculates pKa

8 March 202410 March 2024 chris

A couple of months ago I published a post describing Rowan a web native quantum chemistry package. I just noticed there is an update that

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Macinchem Blog Science Apps Software Reviews

CMD + V for chemistry: Image to chemical structure conversion directly done in the clipboard

2 March 20242 March 2024 chris

This is very cool. Clipboard-to-SMILES Converter (C2SC), is a macOS application that directly converts molecular structures from the clipboard. The app focuses on seamlessly converting

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Macinchem Blog

Molecular shape based similarity

22 February 202415 March 2024 chris

Whilst shape-based complementarity between a ligand and the protein active site are critical for high affinity binding there are very few high performance methods. This

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Macinchem Blog Science Apps

The latest beta of the InChI is now available on GitHub 

19 February 202420 February 2024 chris

This is the first version following transition of the codebase to GitHub, https://github.com/IUPAC-InChI/InChI/releases The change log is available here https://github.com/IUPAC-InChI/InChI/blob/v1.07-beta.3/INCHI-1-DOC/CHANGELOG.md Note they are proposing a

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Macinchem Blog

The Chemical Structure Association grants for 2024

12 February 202412 February 2024 chris

The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. 

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  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    Cambridge Cheminformatics Network Meeting

    Cambridge Cheminformatics Meeting, 22 April 2026 *** AI Agents for Omics *** Chemical Space Docking for Billion-Sized Libraries *** Quantum Chemistry for Protein-Ligand...
  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    mlxmolkit — GPU-accelerated molecular toolkit on Apple Silicon

    I've previously written about mlxmolkit in particular for clustering where see a 40-fold improvement in speed. The toolkit has now...

    https://macinchem.org/2026/04/08/mlxmolkit-gpu-accelerated-molecular-toolkit-on-apple-silicon/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    RSC CICAG Chemical Structure Representations Meeting 2026 

    We do have a lot of different molecular file format, from simple line notations like SMILES to cartesian coordinates (.xyz) to .trexio...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    Avogadro 2.0.0 released

    Avogadro is a free and open source molecular editor and visualization tool. The new release of Avogadro 2, is a major update, and includes major changes, a revised interface,...
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    Looking at mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon

    I've written several posts on the various options for clustering molecules...

    https://macinchem.org/2026/04/03/looking-at-mlxmolkit-gpu-accelerated-molecular-clustering-on-apple-silicon/

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  • RSC CICAG Chemical Structure Representations Meeting 2026 
  • Avogadro 2.0.0 released
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