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Category: Jupyter Notebook

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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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Hints and Tutorials Jupyter Notebook Macinchem Blog Science Apps Vortex Scripts

Using DILIpred

2 March 2025 chris

Drug-induced liver injury (DILI) is a significant concern in drug discovery, in particular because it might only be observed late in large clinical studies, after

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Hints and Tutorials Jupyter Notebook Macinchem Blog Uncategorised Vortex Scripts

Searching Sqlite database from Vortex

26 February 202527 February 2025 chris

In a previous post I illustrated how to download PubChem and create a local searchable database using a Jupyter notebook. I also included a vortex/python

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Vortex Scripts

Searching a local copy of PubChem

17 February 202524 February 2025 chris

PubChem is an invaluable source of information about 99 million molecules accessible via a website or programmatically. PubChem is an open chemistry database at the National Institutes

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Hints and Tutorials Jupyter Notebook Macinchem Blog Science Apps

Calculate pKa using Rowan

8 February 20258 February 2025 chris

Rowan is a software platform that makes it possible to run high-level quantum chemical calculations through a web interface. In general, running quantum chemical calculations

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Software Reviews

Looking at TabPFN

6 February 202517 February 2025 chris

TabPFN is a foundation model  trained on around 130,000,000 synthetically generated datasets that mimic “real world” tabular data. These datasets sampled dataset size and number

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Structure-aware generative molecular design: from 2D or 3D?

20 January 202520 January 2025 chris

A very nice review of generative models for molecular design from Morgan Thomas. https://cheminformantics.blogspot.com/2024/12/structure-aware-generative-molecular.html Includes Jupyter notebooks for data and analysis.

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Jupyter Notebook Other Tips Science Apps Spectroscopy

VeloxChem open-source quantum chemistry software

14 January 202514 January 2025 chris

I just stumbled across this and thought I’d flag it. VeloxChem is a Python-based open source quantum chemistry software developed for the calculation of molecular

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Jupyter Notebook Macinchem Blog Science Apps

ShEPhERD: Shape, Electrostatics, and Pharmacophore Explicit Representation Diffusion

23 November 202423 November 2024 chris

A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design https://arxiv.org/abs/2411.04130v1 …

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Clustering large datasets

13 September 202413 September 2024 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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Avatar Chris Swain @macinchem ·
6 Feb

Looking at TabPFN with Polaris datasets https://macinchem.org/2025/02/06/looking-at-tabpfn/ #cheminformatics

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Avatar RSC_CICAG @rsc_cicag ·
3 Feb

Don't forget to register for @RSC_BMCS Conformation Design in #DrugDiscovery conference on 3rd March! … #chemistry #medicinalchemistry #NMR #computationalchemistry #biologists

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Avatar Rowan @rowansci ·
31 Jan

RDKit is the standard software for cheminformatics, but RDKit doesn’t integrate naturally with high-accuracy chemistry simulation tools.

Starting from RDKit, it's non-trivial to simulate pKa, optimize conformers w/ ML, score tautomers, &c. There are many posts like this:

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Avatar Chris Swain @macinchem ·
31 Jan

Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model on Apple Silicon. https://macinchem.org/2025/01/31/tabpfn-on-apple-silicon/

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