In a previous post I illustrated how to download PubChem and create a local searchable database using a Jupyter notebook. I also included a vortex/python
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
PubChem is an invaluable source of information about 99 million molecules accessible via a website or programmatically. PubChem is an open chemistry database at the National Institutes
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
TabPFN is a foundation model trained on around 130,000,000 synthetically generated datasets that mimic “real world” tabular data. These datasets sampled dataset size and number
A recent paper published in Nature caught my eye, Accurate predictions on small data with a tabular foundation model by Hollmann et al., Here we present
A very nice review of generative models for molecular design from Morgan Thomas. https://cheminformantics.blogspot.com/2024/12/structure-aware-generative-molecular.html Includes Jupyter notebooks for data and analysis.
Whilst Apple’s emulation later Rosetta2 that allows X86_64 applications to run on Apple Silicon this is not ideal especially for computationally intensive tasks. The latest
An interesting publication, using the IUPAC rules for naming compounds can be a challenge for for complex systems. This paper describes a transformer-based model https://doi.org/10.1186/s13321-024-00941-x
A reader asks about running VMD and installing Gromacs on M4 Macs. I don’t use either application and looking on the VMD website there is
Sometimes when I’m comparing multiple datasets I end up with 10-20 different Vortex workspaces, for example if I’m comparing commercial screening collections from different vendors.