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)
Category: Jupyter Notebook
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
In a recent post Pat Walters highlighted the use of molfeat in a google colab notebook https://colab.research.google.com/github/PatWalters/practicalcheminformaticstutorials/blob/main/mlmodels/QSARin8lines.ipynb. I thought I’d also mention other tools available from
FPsim2 is a new tool for fast similarity search on big compound datasets (>100 million) being developed at ChEMBL. It was developed as a Python3 library
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
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,