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Tag: python

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Jupyter Notebook Macinchem Blog

MolSetRep

17 December 202317 December 2023 chris

Cambridge Open Engage is the collaborative platform to upload, share and advance early and open research and a recent post caught my eye. Molecular set

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Macinchem Blog

MLX a machine learning framework for Apple Silicon

8 December 20238 December 2023 chris

I just stumbled across this repository on GitHub, MLX: An array framework for Apple silicon https://github.com/ml-explore/mlx MLX is a NumPy-like array framework designed for efficient

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Hints and Tutorials Macinchem Blog

RDKit MolsMatrixToGridImage

6 December 202312 November 2024 chris

If you need to display molecules and associated data in a grid then Jeremy Monat’s MolsMatrixToGridImage is exactly what you need. To underline just how

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Hints and Tutorials Macinchem Blog

An interesting Cheminformatics blog

22 November 202322 November 2023 chris

Just stumbled across this blog on cheminformatics, machine learning (ML) and data science projects in drug discovery. Lots of useful code! Data in Life https://jhylin.github.io/Data_in_life_blog/

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Hints and Tutorials Uncategorised

Psi4 on Apple Silicon

17 November 202317 November 2023 chris

A couple of folks have asked about the availability of Psi4 on Apple Silicon From Wikipedia Psi is an ab initio computational chemistry package originally written by the research

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Macinchem Blog Other Tips Science Apps

REINVENT4

7 November 20237 November 2023 chris

REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks. At

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Macinchem Blog Science Apps

RDKit update released

16 October 202316 October 2023 chris

2023_09_1 (Q3 2023) Release https://github.com/rdkit/rdkit/releases/tag/Release_2023_09_1 Highlights Plus lots of other changes and enhancements

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Macinchem Blog Science Apps

Lig3DLens An open source ligand-based 3D virtual screening toolbox from Healx

14 October 202314 October 2023 chris

Whilst there are a number of proprietary applications for virtual screening there are few open-source alternatives. Whilst most of the functionality needed is available in

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Data Analysis Tools Hints and Tutorials Macinchem Blog

Scikit-LLM: Sklearn Meets Large Language Models

24 May 202324 May 2023 chris

I just stumbled across this and I thought I’d share it. Seamlessly integrate powerful language models like ChatGPT into scikit-learn for enhanced text analysis tasks.

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Macinchem Blog Science Apps

RDKit updated 2023_03_1 (Q1 2023) Release

2 May 20232 May 2023 chris

Full details here https://github.com/rdkit/rdkit/releases/tag/Release_2023_03_1 Installation injstructions https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md

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    @macinchem.bsky.social 2 days

    nanoFold a Protein Folding Data-Efficiency Competition

    An interesting way to look for better biological foundation models. The core bet is simple: biological data is expensive. Text and image models...

    https://macinchem.org/2026/04/29/nanofold-a-protein-folding-data-efficiency-competition/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    PyChem-Pro

    I've just added PyChem-Pro to the list of cheminformatics toolkits https://macinchem.org/2023/02/17/open-source-cheminformatics-toolkits/ PyChem is a desktop chemistry application and Python library that combines molecular...

    https://macinchem.org/2026/04/27/pychem-pro/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    Open Source Cheminformatics Toolkits

    When I wrote the article entitled A few thoughts on scientific software one of the responses I got was that people did not know about the existence of open-source chemistry...

    https://macinchem.org/2023/02/17/open-source-cheminformatics-toolkits/
  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    Sweet J on Mac App Store

    Calculates the 3J coupling constant from the dihedral angle and the electronegativity of the substituents using either the Altona equation or a generalised Karplus equation. Sweet J can be downloaded...
  • View post by on Bluesky

    @macinchem.bsky.social 7 days

    AI Discovery Awards

    AI Discovery by Nebius is an annual awards for startups that are leveraging AI to revolutionize drug discovery, biotechnology, genomics and HealthTech.. Details are here https://nebius.com/ai-discovery-award...

    https://macinchem.org/2026/04/24/ai-discovery-awards/

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