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Tag: cheminformatics

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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps

Alvascience Tools Now Fully Optimized for Apple Silicon

15 January 202515 January 2025 chris

Whilst Apple’s emulation later Rosetta2 that allows X86_64 applications to run on Apple Silicon this is not ideal especially for computationally intensive tasks. The latest

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Macinchem Blog

RSC CICAG Distillate (formerly Newsletter) now available

15 January 202515 January 2025 chris

The CICAG Newsletter, which had its origins in the 1990s (when CICAG was two groups, the ‘Chemical Information Group’ and the ‘Computer Applications Subject Group’).

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Hints and Tutorials Macinchem Blog Science Apps

STOUT V2.0: SMILES to IUPAC name conversion using transformer models

31 December 202431 December 2024 chris

An interesting publication, using the IUPAC rules for naming compounds can be a challenge for for complex systems. This paper describes a transformer-based model https://doi.org/10.1186/s13321-024-00941-x

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Macinchem Blog Science Apps

AlvaDesc updated

12 December 202412 December 2024 chris

AlvaDesc v3.0.0 has been updated, it has a few new features but for Mac users it is now fully compatible with Apple Silicon!! AlvaDesc is

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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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Hints and Tutorials Macinchem Blog Vortex Scripts

Vortex script to export multiple workspaces to individual sdf files.

19 November 202419 November 2024 chris

Sometimes when I’m comparing multiple datasets I end up with 10-20 different Vortex workspaces, for example if I’m comparing commercial screening collections from different vendors.

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Hints and Tutorials Macinchem Blog

Using lwreg with the RDKit cartridge

31 October 202431 October 2024 chris

Fabulous blog post from Greg Landrum, Includes a tutorial on installing PostgreSQL and the cartridge with conda. This post shows how to use the RDKit

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Hints and Tutorials Macinchem Blog Vortex Scripts

Vortex script for Analysis of Categories

29 October 202429 October 2024 chris

I published a page describing a Vortex script for category analysis that I wrote a while back but I thought I’d mention it because I’m

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Macinchem Blog

Cambridge Cheminformatics Network Meeting

23 October 202423 October 2024 chris

The next Meeting: 13 November 2024, 4-5.30pm UK time, Hybrid (at the CCDC/via Zoom) full details here. Programme My Learnings From Starting Standigm, a Leading

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Macinchem Blog

Feedback from 7th Artificial Intelligence in Chemistry Conference

22 October 202422 October 2024 chris

We have just got the results of the feedback from the 7th RSC-CICAG / RSC-BMCS Artificial Intelligence in Chemistry held at Churchill College in September.

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  • View post by on Bluesky

    @macinchem.bsky.social 19 hours

    OpenBind Blind Challenge: Zika virus NS2B-NS3 protease

    On October 14th the OpenBind Blind Challenge was launched, the target is the Zika virus NS2B-NS3 protease. This challenge focuses on predicting how...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    An Updated Jupyter Notebook for docking

    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] that they all...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    Icms2yield AI-Predicted Full-Spectrum UV Correction Factors: An Analyte-Standard-Free Framework for Reaction Yield Quantification

    https://macinchem.org/2026/10/13/icms2yield-ai-predicted-full-spectrum-uv-correction-factors-an-analyte-standard-free-framework-for-reaction-yield-quantification/
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    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 2 weeks

    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/

Recent Posts

  • OpenBind Blind Challenge: Zika virus NS2B-NS3 protease
  • An Updated Jupyter Notebook for docking
  • Icms2yield AI-Predicted Full-Spectrum UV Correction Factors: An Analyte-Standard-Free Framework for Reaction Yield Quantification
  • Compound Lookup Extensions
  • Building QupKake on Apple Silicon (macOS arm64)
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  • OpenBind Blind Challenge: Zika virus NS2B-NS3 protease
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  • Building QupKake on Apple Silicon (macOS arm64)
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