The latest update of the popular Biomolecular visualisation tool ChimeraX has been released, including some exciting new features, https://www.rbvi.ucsf.edu/chimerax/download.html This update includes – OpenFold3 structure
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
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 —
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
Calculates the 3J coupling constant from the dihedral angle and the electronegativity of the substituents using either the Altona equation or a generalised Karplus equation. Sweet
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
iNMR is a fantastic app for NMR spectroscopy, it has been around for over 20 years and gets better with every release. It has been
I’ve previously written about mlxmolkit in particular for clustering where see a 40-fold improvement in speed. The toolkit has now been extended to include 3D
Avogadro is a free and open source molecular editor and visualization tool. The new release of Avogadro 2, is a major update, and includes major
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