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
Category: Science Apps
Finding scientific applications has always been a little hit and miss since there is no “science” category on the iTunes store. To help out I’ve created a database listing applications that I knew about
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
An update to RDKit has been released 2026_03_1 (Q1 2026). Highlights Note there are a number of backwards incompatible changes. Full details of the release
OpenFold3-preview is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind’sAlphaFold3, developed by the AlQuraishi Lab at Columbia University and the
Just got this message. We’re happy to announce the release of macOS-native MOE 2024.0604 for macOS Tahoe, also compatible with Big Sur and later versions
SpaceLightN is a command line tool from Prof. Rarey (University of Hamburg) for similarity-based virtual screening in large combinatorial fragment spaces. It utilizes well-known fingerprints
BBEdit everyone’s favourite text editor has been updated to 15.5.5 This update contains only fixes for reported symptoms. Please see the release notes for previous versions for
Another addition to the superb MayaChemTools OpenFECalculateRelativeBindingFreeEnergySepTop.py to calculate Relative Binding Free Energy using a Separated Topologies (SepTop) approach. The script relies on the availability of OpenFE
There is an interesting paper in Journal of Cheminformatics J Cheminform 17, 142 (2025). https://doi.org/10.1186/s13321-025-01094-1 Cheminformatics Microservice V3 aims to provide easily accessible and reproducible cheminformatics tools.
The popular chemistry drawing package ChemDoodle has been updated. Version 12.10.0 is a feature update for ChemDoodle 2D. Major additions include a much more powerful