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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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Macinchem Blog Science Apps

BindFlow

29 September 202529 September 2025 chris

Binding free energy calculations are challenging so always good to efforts in this area https://www.biorxiv.org/content/10.1101/2025.09.25.678545v1 We present BindFlow, a Python-based software for automated absolute binding

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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

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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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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Macinchem Blog Other Tips

SureChEMBl update

4 May 2025 chris

If you have been trying to access patent data via SureChEMBL recently you will be very aware that the team have been struggling to provide

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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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Recent Posts

  • Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.
  • OpenADMET Challenge
  • MayaChemTools updated
  • BindFlow
  • ChEMBL 36 is out
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    @macinchem.bsky.social 1 week

    Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.

    https://macinchem.org/2025/10/08/use-the-foundation-models-framework-to-access-the-on-device-llm-that-powers-apple-intelligence/
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    @macinchem.bsky.social 2 weeks

    OpenADMET Challenge

    https://macinchem.org/2025/10/05/openadmet-challenge/
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    @macinchem.bsky.social 2 weeks

    MayaChemTools updated

    https://macinchem.org/2025/10/02/mayachemtools-updated-3/
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    @macinchem.bsky.social 2 weeks

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

    BindFlow – Macs in Chemistry

    macinchem.org

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    @macinchem.bsky.social 2 weeks

    BindFlow

    https://macinchem.org/2025/09/29/bindflow/

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