Project Jupyter is the winner of the White House OSTP “Technical Advancement to Enable Open Science” category. Open science relies on technical advancements and infrastructures
Tag: jupyter
A previous post described Getting Ligand ID for multiple PDB files, using the PDBe API (https://www.ebi.ac.uk/pdbe/pdbe-services). The result is a csv file containing the ligand
The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)
The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)
The previous couple of pages described creating a SQLite database using the Terminal https://macinchem.co.uk/2023/04/12/using-sqlite-for-exact-search/ and then running exact searches from a Jupyter notebook, python script or ChemDraw
The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists
When I wrote the article entitled A few thoughts on scientific software one of the responses I got was that people did not know about the existence
Here are two variations of a Jupyter Notebook to help with docking experiments. The first version runs locally and requires the user to install RDKit,