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Author: chris

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Macinchem Blog

The Chemical Structure Association grants for 2024

12 February 202412 February 2024 chris

The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. 

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Some new ways to speed RDKit calls up using multiple threads

11 February 202411 February 2024 chris

Another tutorial from Greg Landrum, focussing on how to take advantage of modern multithreaded CPUs. https://greglandrum.github.io/rdkit-blog/posts/2024-02-11-more-multithreading.html Looking at Generating fingerprints, Molecular standardization, Conformer generation, RMSD

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Macinchem Blog

Cambridge Cheminformatics Network Meeting 21 Feb 2024

9 February 202410 February 2024 chris

Just thought I would mention that the 3 speakers for the next Cambridge Cheminformatics Network Meeting 21 Feb 2024 meeting have now been finalised so

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Macinchem Blog Science Apps

Small independent developers

7 February 20247 February 2024 chris

I’m always delighted to highlight the efforts of small independent scientific software developers who support MacOS, iOS etc. I wrote iBabel because it was something

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Macinchem Blog Science Apps

Complete HeartX, using spatial computing

6 February 20245 April 2024 chris

As many suggested one of the first uses of the Apple Vision Pro would be education, Complete HeartX allows exploration of 3D models of the

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Macinchem Blog Other Tips

Introducing Pkl, a programming language for configuration

6 February 20246 February 2024 chris

An interesting post from Apple, the open source first release of Pkl (pronounced Pickle), a programming language for producing configuration. There is an introductory blog post

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Macinchem Blog Science Apps

Science Apps for Vision Pro

3 February 20246 February 2024 chris

The Apple Vision Pro could be an interesting device for a variety of areas of science. The first I’ve heard of is CellWalk that allows

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Macinchem Blog Reviews Science Apps Software Reviews

Looking at Rowan a web-native quantum chemistry package

27 January 202428 January 2024 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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Macinchem Blog Science Apps

Flare V8 released

25 January 202425 January 2024 chris

Flare a computer assisted drug design tool from Cresset, in combines an intuitive interface to molecular visualisation, structure-activity analysis and molecular docking with a python

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Uncategorised

A jupyter notebook to download ligands from PDB

24 January 202424 January 2024 chris

A previous post described Getting Ligand ID for multiple PDB files, using the PDBe API (https://www.ebi.ac.uk/pdbe/pdbe-services). The result is a csv file containing the ligand

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Chris Swain Follow

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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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