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Category: Macinchem Blog

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Macinchem Blog Other Tips

Introducing Pkl, a programming language for configuration

6 February 20246 February 2024 chris

An interesting post from Apple, the open source first release of Pkl (pronounced Pickle), a programming language for producing configuration. There is an introductory blog post

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Macinchem Blog Science Apps

Science Apps for Vision Pro

3 February 20246 February 2024 chris

The Apple Vision Pro could be an interesting device for a variety of areas of science. The first I’ve heard of is CellWalk that allows

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Macinchem Blog Reviews Science Apps Software Reviews

Looking at Rowan a web-native quantum chemistry package

27 January 202428 January 2024 chris

Rowan is a software platform that makes it possible to run high-level quantum chemical calculations through a web interface. In general, running quantum chemical calculations

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Macinchem Blog Science Apps

Flare V8 released

25 January 202425 January 2024 chris

Flare a computer assisted drug design tool from Cresset, in combines an intuitive interface to molecular visualisation, structure-activity analysis and molecular docking with a python

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Downloading ligands from the PDB

24 January 202424 January 2024 chris

A previous post described Getting Ligand ID for multiple PDB files, using the PDBe API (https://www.ebi.ac.uk/pdbe/pdbe-services). The result is a csv file containing the ligand

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Macinchem Blog

ChemDoodle updated

23 January 202423 January 2024 chris

Version 12.4.0 is a feature update for ChemDoodle 2D. Included is significant work on IUPAC naming output, support for atropisomer stereochemistry, improved and adjustable crosshair

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Another PDB tools Jupyter Notebook

22 January 202422 January 2024 chris

The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)

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Macinchem Blog

Macintosh at 40.

19 January 202420 January 2024 chris

40 years ago Apple promised that 1984 would not be like “1984” with a stunning Super Bowl ad created by Ridley Scott.

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Macinchem Blog Science Apps

Matched molecular pair database mmpdb 3.1 released

12 January 202412 January 2024 chris

mmpdb 3.0, released May 2023, merged three development tracks: – create and query 1-cut med chem transformations as described in Awale et al., The Playbooks

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Macinchem Blog Science Apps

BBEdit 15 released

11 January 202411 January 2024 chris

BBEdit is my favourite text editor, of lost count of the times I’ve used it to “Zap Gremlins” to remove non-Ascii characters that were invisible

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  • View post by on Bluesky

    @macinchem.bsky.social 2 days

    mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon

    Recently a guest post from NVIDIA described GPU-Accelerated Clustering with nvMolKit that uses CUDA. A recent post no...

    https://macinchem.org/2026/03/11/mlxmolkit-gpu-accelerated-molecular-clustering-on-apple-silicon/
  • View post by on Bluesky

    @macinchem.bsky.social 2 days

    Molecular Docking with Open Access Software

    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. [DOI] This work lead...
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    RSC CICAG Chemical Structure Representation

    AI/ML have reignited our thoughts on how we represent chemical structures and so it is very timely that we have a conference on Structural Representation. Registration...
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    MOE now runs on macOS Tahoe!

    Just got this message. We're happy to announce the release of macOS-native MOE 2024.0604 for macOS Tahoe, also compatible with Big Sur and later versions (minimum version 11.5). The...

    https://macinchem.org/2026/03/09/moe-now-runs-on-macos-tahoe/
  • View post by on Bluesky

    @macinchem.bsky.social 7 days

    I'm in London for the RSC BMCS committee meeting. Looking around Burlington House I'm reminded what a great venue this is for scientific meetings. The next one I'll be at is Analyticode 2006 on 16 March 2026 www.rsc.org/events/detai.... Still time to register.

Recent Posts

  • PDB reaches a quarter of a million structures
  • mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon
  • Molecular Docking with Open Access Software
  • RSC CICAG Chemical Structure Representation
  • MOE now runs on macOS Tahoe!
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