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
Tag: python
This looks very useful. dock-postprocess is an open-source structure-based drug design toolkit for standardizing docking results and carrying them through restrained OpenMM minimization, pose QC, protein-ligand
I just stumbled across this when looking for something else. It looks very interesting A pure-Python desktop application and library for chemistry and cheminformatics —
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 just added PyChem-Pro to the list of cheminformatics toolkits https://macinchem.org/2023/02/17/open-source-cheminformatics-toolkits/ PyChem is a desktop chemistry application and Python library that combines molecular visualization (like
A recent paper on ChemRxiv https://chemrxiv.org/doi/10.26434/chemrxiv-2025-9c1v6 describes ANNalog a transformer-based sequence-to-sequence generative model trained on pairs of molecules extracted from the same bioactivity assay in
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
Mole2D is a lightweight molecule drawing package written in Python and PyQt6. All code is on GitHub https://github.com/sfmlab/mole2d and it requires RDKit and PyQt6.. PubChem
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
In 2020 as a result of lockdown I was asked to help create a course for MRes students as an introduction to computer-aided drug design.