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Author: chris

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Applescript Hints and Tutorials

Getting started with AppleScript

6 March 202326 October 2023 chris

This is the first of what will hopefully be a series of tutorials on Apple’s own scripting language Applescript. I should perhaps begin with a

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Hints and Tutorials Vortex Scripts

Vortex script using Openbabel for similarity searching

6 March 202315 May 2023 chris

An earlier script showed how to calculate molecular similarity between the first molecule in the file and all the other molecules using OpenBabel as shown

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Hints and Tutorials Vortex Scripts

Vortex script using MOE to calculate properties

6 March 202321 June 2023 chris

MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means

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Hints and Tutorials Vortex Scripts

Vortex script to analyze categories

5 March 202312 April 2023 chris

I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver

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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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Data Analysis Tools Hints and Tutorials Vortex Scripts

Calculating molecular properties using the ChemAxon cxcalc

4 March 202325 April 2023 chris

ChemAxon’s Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a

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Hints and Tutorials Vortex Scripts

Scripting Vortex and OpenBabel

4 March 202312 April 2023 chris

I’m finding that I using Vortex more and more in my day job, it is an excellent application for displaying and exploring large or complex

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Data Analysis Tools Hints and Tutorials

Knime Tutorial

4 March 202315 April 2023 chris

This tutorial was kindly provided by Greg a Macinchem reader. OVERVIEW AND APPLICATION OF KNIME AND CDKDescUI.jar KNIME1, the Konstanz Information Miner, is a visual platform

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Macinchem Blog Reviews Science Apps Software Reviews

ChemDoodle Review

4 March 202311 May 2023 chris

ChemDoodle 3.0 from iChemLabs is the latest update of a chemical drawing package that also provides for support for many other types of chemical data such

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Hints and Tutorials Macinchem Blog Reviews Software Reviews

ChemDoodle Web Components

4 March 202312 April 2023 chris

Introduction and Background ChemDoodle Web Components are pure javascript objects derived from ChemDoodle™ to solve common chemistry related tasks on the web. These components are powerful,

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    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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    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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    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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    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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