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Tag: python

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Hints and Tutorials Macinchem Blog Vortex Scripts

Two Vortex scripts for interacting with PDB

5 April 20255 April 2025 chris

The Worldwide Protein Data Bank collects, organises and disseminates data on biological macromolecular structures. The wwPDB Partners are: PDBe, RCSB PDB, PDBj, BMRB, EMDB. Currently the PDB contains over

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Hints and Tutorials Macinchem Blog

Cheminformatics tools that work natively with Google tools such as Sheets and BigQuery

31 March 202531 March 2025 chris

Whilst there are a number of chemistry aware spreadsheets Vortex, Stardrop, Datawarrior, InstantJChem, molsoft etc. many people still use Excel or Google sheets. Vexo is

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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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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps Software Reviews

TabPFN on Apple Silicon

31 January 202531 January 2025 chris

A recent paper published in Nature caught my eye, Accurate predictions on small data with a tabular foundation model by Hollmann et al., Here we present

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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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Macinchem Blog Science Apps

AlvaDesc updated

12 December 202412 December 2024 chris

AlvaDesc v3.0.0 has been updated, it has a few new features but for Mac users it is now fully compatible with Apple Silicon!! AlvaDesc is

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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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    OpenADMET Challenge

    https://macinchem.org/2025/10/05/openadmet-challenge/
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    MayaChemTools updated

    https://macinchem.org/2025/10/02/mayachemtools-updated-3/
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    This looks interesting, binding free energy calculations macinchem.org/2025/09/29/b...

    BindFlow – Macs in Chemistry

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    BindFlow

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

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