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Tag: cheminformatics

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Macinchem Blog Reviews Science Apps

A Review of ChemDoodle 7

10 October 202310 October 2023 chris

ChemDoodle is now firmly established as one of the key chemical drawing packages that offers an inexpensive alternative to some of the increasingly expensive drawing

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Macinchem Blog Uncategorised

Cambridge Cheminformatics Network Meeting

15 September 202319 September 2023 chris

20 September 2023, 4-5.30pm UK time, Hybrid (at the CCDC/via Zoom) Zoom registration here: https://zoom.us/meeting/register/tJIqf-qhqjktHtSPZ0jtztLwDWnbp3CxmqUn Programme: Benchmarking Structure-Based 3D Molecular Generative Models Benoit Baillif, University

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Macinchem Blog Other Tips

New PyMOL script

31 July 202331 July 2023 chris

I just got details of a new script for PyMOL. The script PyMOLVisualizeFpockets.py relies on the presence of PyMOL in your environment and provides functionality to

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Macinchem Blog

Summer 2023 CICAG newsletter

12 July 202312 July 2023 chris

The latest Royal Society of Chemistry Chemical Information and Computer Applications interest group (http://www.rsccicag.org) newsletter is now available. It can be found on the CICAG

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Macinchem Blog Science Apps

alvaBuilder

5 July 20235 July 2023 chris

AlvaBuilder is a software tool for de novo molecular design (Mauri, A., Bertola, M. (2023). AlvaBuilder: A Software for De Novo Molecular Design. https://doi.org/10.1021/acs.jcim.3c00610; Mauri, A.,

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Macinchem Blog

7 June 2023 Cambridge Cheminformatics Network Meeting

30 May 202330 May 2023 chris

In person at the Cambridge Crystallographic Data Centre on Union Road, Cambridge. 7 June 2023, 4-5.30pm UK time. Social event afterwards at the Alma.Registration (for Zoom

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Macinchem Blog Science Apps

ChemDoodle 2D v12 is Unveiled

15 May 202315 May 2023 chris

iChemLabs have just announced the release of the hugely popular ChemDoodle 2D v12. https://ichemlabs.com/news/read?post=cd12_released ChemDoodle 2D v12 presents a new, refreshed interface. We took a

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Macinchem Blog Science Apps

RDKit updated 2023_03_1 (Q1 2023) Release

2 May 20232 May 2023 chris

Full details here https://github.com/rdkit/rdkit/releases/tag/Release_2023_03_1 Installation injstructions https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md

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Macinchem Blog Science Apps

alvaScience updates

20 April 202322 April 2023 chris

alvaBuilder v1.0.10: alvaDesc v2.0.16: alvaModel v2.0.8: alvaMolecule v2.0.6: alvaRunner v2.0.8:

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Hints and Tutorials Jupyter Notebook Other Tips

Structure-based searching SQLite database

12 April 202318 February 2025 chris

The previous couple of pages described creating a SQLite database using the Terminal https://macinchem.co.uk/2023/04/12/using-sqlite-for-exact-search/ and then running exact searches from a Jupyter notebook, python script or ChemDraw

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    @macinchem.bsky.social 3 days

    RSC CICAG Chemical Structure Representations Meeting 2026 

    This meeting will be held at Burlington House, London, UK on Wednesday 8th April 2026. A one-day conference on Chemical Structure...
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    @macinchem.bsky.social 4 days

    OpenADMET Blind Challenge: Predicting PXR Induction

    The next OpenADMET blind challenge focuses on predicting human Pregnane-X Receptor (hPXR) induction. The pregnane X receptor (hPXR) is the major...
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    @macinchem.bsky.social 6 days

    OpenFold3-preview

    OpenFold3-preview is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind'sAlphaFold3, developed by the AlQuraishi Lab at Columbia University and the OpenFold consortium. This research...
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    @macinchem.bsky.social 1 week

    SCORE MLX Distilled CheMeleon molecular fingerprints on Apple Silicon

    ChemeleonSMD distills the CheMeleon pretrained Directed Message Passing Neural Network (DMPNN) into a SCORE-style...

    https://macinchem.org/2026/03/14/score-mlx-distilled-chemeleon-molecular-fingerprints-on-apple-silicon/
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    PDB reaches a quarter of a million structures

    The Protein Data Bank is an invaluable resource for protein structural information. As well as being a resource used by structural biologists, medicinal chemists and...

    https://macinchem.org/2026/03/12/pdb-reaches-a-quarter-of-a-million-structures/
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  • RSC CICAG Chemical Structure Representations Meeting 2026 
  • OpenADMET Blind Challenge: Predicting PXR Induction
  • OpenFold3-preview
  • SCORE MLX Distilled CheMeleon molecular fingerprints on Apple Silicon
  • PDB reaches a quarter of a million structures
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