I’m sometimes asked for a tool to compare the similarity of a list of molecules with every other molecule in the list. I suspect there
Category: Jupyter Notebook
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
Another tutorial from Greg Landrum, focussing on how to take advantage of modern multithreaded CPUs. https://greglandrum.github.io/rdkit-blog/posts/2024-02-11-more-multithreading.html Looking at Generating fingerprints, Molecular standardization, Conformer generation, RMSD
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)
Scikit-Mol originated during an RDKit hackathon and has gradually evolved into a tool that I looks extremely useful. Scikit-Mol is related to Scikit-learn and molecules,
Cambridge Open Engage is the collaborative platform to upload, share and advance early and open research and a recent post caught my eye. Molecular set
Great to hear about the release of BioSimSpace and sire 2023.4.0. New features in sire include support for running alchemical relative free energy calculations directly
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