The two previous vortex scripts used the PBD id to download information about a biomolecular structure structure from the Worldwide Protein Data Bank. The second
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
The Worldwide Protein Data Bank collects, organises and disseminates data on biological macromolecular structures. The wwPDB Partners are: PDBe, RCSB PDB, PDBj, BMRB, EMDB. Currently the PDB contains over
Whilst there are a number of chemistry aware spreadsheets Vortex, Stardrop, Datawarrior, InstantJChem, molsoft etc. many people still use Excel or Google sheets. Vexo is
Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups
Drug-induced liver injury (DILI) is a significant concern in drug discovery, in particular because it might only be observed late in large clinical studies, after
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
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