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Category: Other Tips

Other tips or tutorials

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Data Analysis Tools Other Tips

Virtual screening/Docking workflow

11 March 20234 February 2026 chris

Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the lack of accessibility of a

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Hints and Tutorials Other Tips

Downloading from PDB using Python

11 March 202312 April 2023 chris

The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists

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Hints and Tutorials Other Tips Science Apps

ChemDraw Advanced User tips

9 March 202324 May 2023 chris

If you are a regular user of ChemDraw you may be aware of the keyboard shortcuts that enable to quickly enter chemical structures.In fact there

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Applescript Hints and Tutorials Other Tips

Combining PDFs using an Automator Workflow

6 March 202318 May 2023 chris

Today I was sent a license agreement as a 6 page pdf file, I was asked to sign the document and send it back. All

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Hints and Tutorials Other Tips

Preview Tips

6 March 202311 May 2023 chris

PDF seems to have become the standard for online distribution of publications, this is despite many obvious limitations. In particular from the point of view

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Hints and Tutorials Other Tips Vortex Scripts

Options for Clustering large datasets of Molecules

5 March 202310 April 2025 chris

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that

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Hints and Tutorials Other Tips

Useful Unix commands

18 February 202321 April 2023 chris

I’m regularly handling very large files containing millions for chemical structures and whilst BBEdit is my usual tool for editing text files in practice it

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  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    Using t-SNE to provide an interactive visualisation

    t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in...
  • View post by on Bluesky

    @macinchem.bsky.social 5 days

    SpaceLightN

    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 methods such as the...

    https://macinchem.org/2026/03/02/spacelightn/
  • View post by on Bluesky

    @macinchem.bsky.social 5 days

    Apply to lead a strategic research lab dedicated to fundamental artificial intelligence (AI) development. 

    https://macinchem.org/2026/03/02/apply-to-lead-a-strategic-research-lab-dedicated-to-fundamental-artificial-intelligence-ai-development/
  • View post by on Bluesky

    @macinchem.bsky.social 7 days

    Fortran on a Mac

    I've updated the Fortran on a Mac page https://macinchem.org/fortran-on-a-mac/ Now includes gcc-15.2-mx-bin.tar.gz, gfortran-15.2-mx-bin.tar.gz (gfortran only), updated Jan 2026 (Tahoe — Apple...

    https://macinchem.org/2026/02/28/fortran-on-a-mac-3/
  • View post by on Bluesky

    @macinchem.bsky.social 7 days

    CHEMBL2ML

    An interesting web app that fetches ChEMBL bioactivity data for a target (via UniProt ID), computes molecular descriptors, and trains a simple predictive model (regression, with an optional classification fallback)....

    https://macinchem.org/2026/02/28/chembl2ml/
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