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Category: Hints and Tutorials

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Hints and Tutorials Macinchem Blog

MayaChemTools updated

2 October 20252 October 2025 chris

The excellent MayChemTools has been updated 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

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Data Analysis Tools Hints and Tutorials Macinchem Blog

ChEMBL 36 is out

26 September 202526 September 2025 chris

One of the most useful databases for anyone involved in studies involved in biologically active molecules. ChEMBL is a manually curated database of bioactive molecules

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Hints and Tutorials Jupyter Notebook Macinchem Blog

SimpleFold: Folding Proteins is Simpler than You Think

24 September 202524 September 2025 chris

Apple just posted preprint on arxiv describing a new protein structure prediction tool SimpleFold https://arxiv.org/pdf/2509.18480. All code is available on GitHub https://github.com/apple/ml-simplefold including a simple

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Hints and Tutorials Macinchem Blog

XQuartz and macOS Tahoe

18 September 202519 September 2025 chris

A couple of readers have mentioned issues with using XQuartz after upgrading to macOS Tahoe. Looking on GitHub there are a couple issues. https://github.com/XQuartz/XQuartz/issues/446 https://github.com/XQuartz/XQuartz/issues/438

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Hints and Tutorials Macinchem Blog

nvMolKit: a core set of GPU-accelerated RDKit functions

11 September 202518 September 2025 chris

An interesting post from Nvidia. nvMolKit, is a standalone, GPU-accelerated library that delivers 1-4 orders of magnitude of acceleration across five key functions: Morgan Fingerprinting,

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Hints and Tutorials Macinchem Blog Science Apps

KNIME in cheminformatics

25 August 202511 September 2025 chris

A recent excellent blog post highlighted the use of a KNIME workflow. KNIME https://www.knime.com is a workflow platform that can be used for many cheminformatics

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Hints and Tutorials Macinchem Blog Science Apps

ORCA Python Interface

16 August 2025 chris

The ORCA Python Interface (OPI) is a Python library to create input and parse output of ORCA. It is designed as an open source community effort

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Data Analysis Tools Hints and Tutorials Macinchem Blog Vortex Scripts

Selecting random clusters from a large dataset in Vortex

18 July 2025 chris

When making selections from large datasets it is worth mentioning that as datasets get larger a simple random selection is often the best (and quickest)

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Applescript Hints and Tutorials Macinchem Blog

Using ChemDraw as input for Boltz docking

11 July 202511 July 2025 chris

A recent paper described Boltz-1: Democratizing Biomolecular Interaction Modeling https://www.biorxiv.org/content/10.1101/2024.11.19.624167v2 Boltz-1, an open-source deep learning model incorporating innovations in model architecture, speed optimization, and data processing

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Hints and Tutorials Macinchem Blog Science Apps

Boltz on Apple Silicon

17 June 202518 June 2025 chris

A recent paper described Boltz-1: Democratizing Biomolecular Interaction Modeling https://www.biorxiv.org/content/10.1101/2024.11.19.624167v2 Boltz-1, an open-source deep learning model incorporating innovations in model architecture, speed optimization, and data

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    OpenADMET Challenge

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    MayaChemTools updated

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    This looks interesting, binding free energy calculations macinchem.org/2025/09/29/b...

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    BindFlow

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    I've now included a Bluesky feed onto the website. macinchem.org

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