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Tag: cheminformatics

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Macinchem Blog Other Tips Science Apps

RDKit Updated

28 March 202628 March 2026 chris

An update to RDKit has been released 2026_03_1 (Q1 2026). Highlights Note there are a number of backwards incompatible changes. Full details of the release

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Data Analysis Tools Hints and Tutorials Macinchem Blog Vortex Scripts

Uniprot ID to target name and bio activities

26 March 202626 March 2026 chris

Sometimes target identification studies can just turn up a list of Uniprot IDs, whilst there are a number of places you can go to find

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Macinchem Blog meetings

RSC CICAG Chemical Structure Representations Meeting 2026 

18 March 20262 April 2026 chris

This meeting will be held at Burlington House, London, UK on Wednesday 8th April 2026. A one-day conference on Chemical Structure Representations will bring together

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Data Analysis Tools Macinchem Blog

OpenADMET Blind Challenge: Predicting PXR Induction

17 March 202617 March 2026 chris

The next OpenADMET blind challenge focuses on predicting human Pregnane-X Receptor (hPXR) induction. The pregnane X receptor (hPXR) is the major determinant of CYP3A gene regulation by

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Data Analysis Tools Macinchem Blog

SCORE MLX Distilled CheMeleon molecular fingerprints on Apple Silicon

14 March 202614 March 2026 chris

ChemeleonSMD distills the CheMeleon pretrained Directed Message Passing Neural Network (DMPNN) into a SCORE-style architecture running natively on MLX. The SCORE Euler skip connection replaces ChemProp’s hard-overwrite message passing

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Hints and Tutorials Macinchem Blog

mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon

11 March 202611 March 2026 chris

Recently a guest post from NVIDIA described GPU-Accelerated Clustering with nvMolKit that uses CUDA. A recent post no describes a port of the nvMolKit (CUDA) molecular clustering

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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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Macinchem Blog meetings

RSC CICAG Chemical Structure Representation

10 March 202610 March 2026 chris

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.

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Vortex Scripts

Using t-SNE and Vortex to provide an interactive visualisation

4 March 20264 March 2026 chris

t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in a two or three-dimensional map. Whilst there are

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Macinchem Blog Science Apps

SpaceLightN

2 March 20262 March 2026 chris

SpaceLightN is a command line tool from Prof. Rarey (University of Hamburg) for similarity-based virtual screening in large combinatorial fragment spaces. It utilizes well-known fingerprints

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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 4 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 4 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 6 days

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