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Macinchem Blog Uncategorised

Frontier AI: SME Champions, phase 1

6 October 20266 October 2026 chris

UK registered micro, small or medium sized enterprise (SMEs) can apply for a share of up to £3.1 million to deliver feasibility studies for frontier

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Hints and Tutorials Jupyter Notebook Macinchem Blog Science Apps Software Reviews Uncategorised

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

3 April 20265 April 2026 chris

I’ve written several posts on the various options for clustering molecules https://macinchem.org/?s=clustering and a recent post from NVIDIA described GPU-Accelerated Clustering with nvMolKit that uses

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Hints and Tutorials Jupyter Notebook Macinchem Blog Uncategorised

Molecular Docking with Open Access Software

10 March 202618 March 2026 chris

In 2020 as a result of lockdown I was asked to help create a course for MRes students as an introduction to computer-aided drug design.

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Hints and Tutorials Jupyter Notebook Macinchem Blog Uncategorised Vortex Scripts

PROTAC-Splitter: A Machine Learning Framework for Automated Identification of PROTAC Substructures

11 February 202614 February 2026 chris

PROteolysis TArgeting Chimeras (PROTACs) technology provides an alternative to module biological function by specially using the ubiquitin proteasome system to induce degradation of the target

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Macinchem Blog Uncategorised

UK researcher high performance computing facilities: spring 2025

25 March 202525 March 2025 chris

This opportunity provides an open and flexible route to computational support for high quality projects across the entire UK Research and Innovation (UKRI) remit. Details

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Hints and Tutorials Jupyter Notebook Macinchem Blog Uncategorised Vortex Scripts

Searching Sqlite database from Vortex

26 February 202527 February 2025 chris

In a previous post I illustrated how to download PubChem and create a local searchable database using a Jupyter notebook. I also included a vortex/python

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Macinchem Blog Other Tips Science Apps Uncategorised

Mychem a chemoinformatics extension for MySQL

9 February 20259 February 2025 chris

Mychem is a chemoinformatics extension for MySQL that provides a set of functions that handles chemical data stored in a database. Mychem is based on

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Macinchem Blog Uncategorised

Latest Cache Challenge

17 June 202417 June 2024 chris

The latest (6th) Cache challenge has been released. The target is SETDB1 Participants are asked to find molecules occupying one or multiple subcavities of the

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Macinchem Blog Uncategorised

Apple Intelligence an approach to AI privacy?

11 June 202411 June 2024 chris

This weeks WWDC gave details of upgrades to the various operating systems. Great to see the calculator make it to the iPad at last, the

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Macinchem Blog Science Apps Uncategorised

PyMOL 3.0 New Features

28 March 202428 March 2024 chris

An excellent brief introduction to PyMOL 3.0.

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Posts pagination

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  • View post by on Bluesky

    @macinchem.bsky.social 2 days

    Compound Lookup Extensions

    I just noticed that the Compound Lookup extensions have been downloaded over 100 times (Safari + Chrome) and I've received some positive feedback.. I'm delighted that such a niche...

    https://macinchem.org/2026/10/11/compound-lookup-extensions/
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    Building QupKake on Apple Silicon (macOS arm64)

    QupKake predicts micro-pKa values with GFN2-xTB plus graph neural networks. Its README targets Linux. On an Apple Silicon Mac the obvious routes all fail: The...

    https://macinchem.org/2026/10/10/building-qupkake-on-apple-silicon-macos-arm64/
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    A collection of Python scripts for PyMOL

    Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also...
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    The latest session in the BMCS Hot Topics online meeting is entitled "AI in Drug Discovery" and has a fantastic lineup of speakers. Registration is open cambridgemedchemconsulting.com/2026/10/09/a...
  • View post by on Bluesky

    @macinchem.bsky.social 5 days

    BMCS New Approaches to Neurodegenerative Diseases cambridgemedchemconsulting.com/2026/10/07/b...

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  • Building QupKake on Apple Silicon (macOS arm64)
  • A collection of Python scripts for PyMOL
  • Frontier AI: SME Champions, phase 1
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