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Author: chris

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Hints and Tutorials Macinchem Blog Vortex Scripts

Uniprot to PDB id Vortex script

13 April 202513 April 2025 chris

The previous scripts have allowed the user to get more information about a PDB entry and to import the ligand structures. This script allows the

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Hints and Tutorials Jupyter Notebook Macinchem Blog Software Reviews

BitBirch update

10 April 202510 April 2025 chris

I’ve written a comparison of various clustering tools including BitBirch. A recent preprint [DOI] has illustrated BitBIRCH Clustering Refinement Strategies. In this Application Note we

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Macinchem Blog Other Tips

MayaChemTools Updated

9 April 202518 April 2025 chris

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs. The new release contained three new python

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Data Analysis Tools Hints and Tutorials Macinchem Blog Vortex Scripts

Vortex script for getting PDB ligand structures

6 April 20256 April 2025 chris

The two previous vortex scripts used the PBD id to download information about a biomolecular structure structure from the Worldwide Protein Data Bank. The second

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Hints and Tutorials Macinchem Blog Vortex Scripts

Two Vortex scripts for interacting with PDB

5 April 20255 April 2025 chris

The Worldwide Protein Data Bank collects, organises and disseminates data on biological macromolecular structures. The wwPDB Partners are: PDBe, RCSB PDB, PDBj, BMRB, EMDB. Currently the PDB contains over

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Hints and Tutorials Macinchem Blog

Cheminformatics tools that work natively with Google tools such as Sheets and BigQuery

31 March 202531 March 2025 chris

Whilst there are a number of chemistry aware spreadsheets Vortex, Stardrop, Datawarrior, InstantJChem, molsoft etc. many people still use Excel or Google sheets. Vexo is

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Macinchem Blog meetings

 Cambridge Cheminformatics Meeting on 23 April 2025

31 March 202531 March 2025 chris

Programme A Day in the Life of a Chief Data Science Officer: Making Data-Driven Decisions in Drug Discovery Layla Hosseini-Gerami, Ignota Labs https://www.ignotalabs.ai Targeting the

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Macinchem Blog Uncategorised

UK researcher high performance computing facilities: spring 2025

25 March 202525 March 2025 chris

This opportunity provides an open and flexible route to computational support for high quality projects across the entire UK Research and Innovation (UKRI) remit. Details

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Macinchem Blog meetings

Researcher Collaborations Grant

18 March 202525 March 2025 chris

RSC Researcher Collaborations Grant enables researchers to establish and develop national, international, interdisciplinary and cross-sector collaborations and networks. RSC members can apply for funding to

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Hints and Tutorials Science Apps

Checkmol

8 March 202525 March 2025 chris

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups

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  • View post by on Bluesky

    @macinchem.bsky.social 1 day

    Generation of MedChem-similar Molecules

    A recent paper on ChemRxiv https://chemrxiv.org/doi/10.26434/chemrxiv-2025-9c1v6 describes ANNalog a transformer-based sequence-to-sequence generative model trained on pairs of...

    https://macinchem.org/2026/04/17/generation-of-medchem-similar-molecules/
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    A few upcoming meetings that may be of interest

    Cambridge Cheminformatics Meeting Cambridge Cheminformatics Meeting, 22 April 2026 *** AI Agents for Omics *** Chemical Space Docking for Billion-Sized Libraries...

    https://macinchem.org/2026/04/15/a-few-upcoming-meetings-that-may-be-of-interest/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    iNMR updated 7.1.1 released

    iNMR is a fantastic app for NMR spectroscopy, it has been around for over 20 years and gets better with every release. It has been compiled for the Apple...

    https://macinchem.org/2026/04/14/inmr-updated-7-1-1-released/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    Cambridge Cheminformatics Network Meeting

    Cambridge Cheminformatics Meeting, 22 April 2026 *** AI Agents for Omics *** Chemical Space Docking for Billion-Sized Libraries *** Quantum Chemistry for Protein-Ligand...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    mlxmolkit — GPU-accelerated molecular toolkit on Apple Silicon

    I've previously written about mlxmolkit in particular for clustering where see a 40-fold improvement in speed. The toolkit has now...

    https://macinchem.org/2026/04/08/mlxmolkit-gpu-accelerated-molecular-toolkit-on-apple-silicon/

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  • Generation of MedChem-similar Molecules
  • A few upcoming meetings that may be of interest
  • iNMR updated 7.1.1 released
  • Cambridge Cheminformatics Network Meeting
  • mlxmolkit — GPU-accelerated molecular toolkit on Apple Silicon
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