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Tag: machine learning

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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

AI Club for Biomedicine

16 January 202616 January 2026 chris

Next up Date: 5 February 2026 Lecture Theatre, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW. No need to register in advance – just

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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps

TabPFN-2.5

10 November 202510 November 2025 chris

I’ve reviewed TabPFN in the past. https://macinchem.org/2025/02/06/looking-at-tabpfn and I noticed there was a recent update. TabPFN is a foundation model  trained on around 130,000,000 synthetically generated

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Hints and Tutorials Macinchem Blog

Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.

8 October 2025 chris
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Macinchem Blog

OpenADMET Challenge

5 October 20255 October 2025 chris

OpenADMET have just announced the ExpansionRx-OpenADMET blind challenge in partnership with Expansion Therapeutics. Expansion Therapeutics have decided to make all the ADMET publicly available. “We

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Software Reviews

Looking at TabPFN

6 February 202517 February 2025 chris

TabPFN is a foundation model  trained on around 130,000,000 synthetically generated datasets that mimic “real world” tabular data. These datasets sampled dataset size and number

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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps Software Reviews

TabPFN on Apple Silicon

31 January 202531 January 2025 chris

A recent paper published in Nature caught my eye, Accurate predictions on small data with a tabular foundation model by Hollmann et al., Here we present

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Jupyter Notebook Macinchem Blog Science Apps

ShEPhERD: Shape, Electrostatics, and Pharmacophore Explicit Representation Diffusion

23 November 202423 November 2024 chris

A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design https://arxiv.org/abs/2411.04130v1 …

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Data Analysis Tools Macinchem Blog

ReALM: Reference Resolution As Language Modeling

2 April 2024 chris

A new Apple preprint has appeared on Arxiv. https://arxiv.org/pdf/2403.20329.pdf Reference resolution is an important problem, one that is essential to understand and success- fully handle

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Macinchem Blog Science Apps

RoseTTAFold All-Atom is published

8 March 20248 March 2024 chris

I suspect many people have been anticipating this, whilst AlphaFold was a great step forward in predicting protein 3D structure it did have significant limitations.

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  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    ChemDoodle Update

    ChemDoodle 2D has been updated. The main focus is expanded support for inorganic compounds and complexes, including haptic bonds and multi-center attachments, their use in formula and mass calculations,...

    https://macinchem.org/2026/09/20/chemdoodle-update/
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    AlvaSketcher

    There a number of chemical drawing packages around that range from lightweight apps for providing structure input to database searches to large fully features packages designed to provide publication...
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    dock-postprocess

    This looks very useful. dock-postprocess is an open-source structure-based drug design toolkit for standardizing docking results and carrying them through restrained OpenMM minimization, pose QC, protein-ligand...

    https://macinchem.org/2026/09/07/dock-postprocess/
  • View post by on Bluesky

    @macinchem.bsky.social 4 weeks

    Updated Mac mini and Mac Studio

    Apple have announced new Mac mini and Mac Studio machines. Mac mini has either M5 Pro chip or M6 chip M5 Pro 15‑core CPU with 5 super cores and 10 performance...

    https://macinchem.org/2026/08/26/updated-mac-mini-and-mac-studio/
  • View post by on Bluesky

    @macinchem.bsky.social 4 weeks

    Installing the OpenADMET PXR anvil prediction

    I had a couple of issues installing the PXR model from OpenAMET on my Apple Silicon Mac (https://huggingface.co/openadmet/pxr-chemeleon-baseline) so I thought I'd...

    https://macinchem.org/2026/08/25/installing-the-openadmet-pxr-anvil-prediction/
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