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
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
This a Google Chrome Extension, it allows you so select a drug name in a web page (for example), right-click and from the dropdown menu
I had a couple of issues installing the PXR model from OpenAMET on my Apple Silicon Mac (https://huggingface.co/openadmet/pxr-chemeleon-baseline) so I thought I’d post what I
mlxmolkit is a GPU-accelerated molecular toolkit on Apple Silicon, it is a port of nvMolKit that uses Cuda. There are now three pipelines Full details
How often have you found a structure file on your desktop and wondered what it contained? You could open it in the relevant software application
For a long time the computational chemistry and molecular modelling package MOE from Chemical Computing Group has required XQuartz to provide the windowing environment. With
I’ve written about TabPFN previously https://macinchem.org/2025/02/06/looking-at-tabpfn/ and I see a technical report has just been published. https://priorlabs.ai/technical-reports/tabpfn-3 TabPFN is a foundation model trained on around 130,000,000
https://www.linkedin.com/feed/update/urn:li:activity:7461059877155631105 A fantastic step-by-step breakdown of an example Python pipeline used to build a ligand-based 3D pharmacophore model using free, open-source tools.
I’ve written several posts on the various options for clustering molecules https://macinchem.org/?s=clustering and a recent post from NVIDIA described GPU-Accelerated Clustering with nvMolKit that uses
Sometimes target identification studies can just turn up a list of Uniprot IDs, whilst there are a number of places you can go to find