CompChem Tools

Computational Chemistry Tools

Whilst there are number of Open Source computational toolkits and command-line tools they often present a step learning curve for new users. In an effort to provide a simpler environment to access these tools this page will highlight a series of Jupyter notebooks that users can use to run key computational studies that might be undertaken in a drug discovery project.

To use these notebooks you will need to have Jupyter and a number of Python libraries installed. The easiest way to do this is to use Anaconda. Anaconda is a modern package manager and seems to be becoming the preferred source of scientific software.

Install Conda using the instructions here https://www.anaconda.com/distribution/

Then in a terminal window type

conda install jupyter
conda install -c rdkit rdkit
conda install numpy
conda install scipy
conda install scikit-learn
conda install pandas
conda install matplotlib
conda install seaborn

A Jupyter Notebook to aid Docking to MurD protein

This notebook implements a typical protocol for docking ligands to a target protein. It uses RDKit (http://www.rdkit.org) to generate a number of reasonable conformations for each ligand and then uses SMINA (https://sourceforge.net/projects/smina/) to do the docking. Two methods of docking are implemented, the first docks into a rigid receptor, the second sets the protein side-chains around the active site to be flexible. Bear in mind flexible docking will be much, much slower. In the optional final step the resulting docked poses are rescored using a random forest model described in this publication DOI. You can read more details of the notebook here and you can download a folder containing the notebook and the necessary files here.

A Jupyter Notebook to access structures and data from the master worksheet

This notebook demonstrates how to get the structures and data from the master worksheet, then convert the SMILES to molecule objects using RDKit that allow some simple manipulisations and visualisations. SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html You can read more details of the notebook here and you can download the notebook here.