A collection of colabs useful for molecular biology tasks. See blog.booleanbiotech.com for more details.

This colab allows you to dock a ligand to a protein with DiffDock, refines the docked position with gnina, displays the result in the notebook, and downloads all the outputs.

This colab allows you to run a simple MD simulation of a protein and a ligand, displays the result in the notebook, and downloads all the outputs. The code is from https://github.com/hgbrian/MD_protein_ligand.

Consider using this making-it-rain colab also.

This colab takes as input a SMILES and returns predicted properties, using chemprop.

A simple colab that turns a PDB file into a high-quality PNG using pymol. The code is from https://github.com/hgbrian/pdb2png.

A basic colab for running Pocket2Mol. Pocket2Mol generates a small molecule to fit a specific pocket.