One cool feature in rdkit is the ability to visually highlight the similarity between two given molecules. In another post (Tanimoto Molecular Similarity Experiment) we saw how to find similar molecules using Tanimoto and Morgan Fingerprints. At the end of the experiment we created an image file with the top 20 similar molecules to D-Aspartate … Continue reading Mapping molecule similarity using rdkit
Category: Chemoinformatics
Chemoinformatics
Painting molecules using rdkit and iPython Notebook
A common requirement when working with molecules is to display their molecular structure as an image. To do this in iPython Notebook requires some simple steps. Below is a way how you can do it. Enjoy! %matplotlib inline %pylab inline from IPython.display import Image from rdkit.Chem import AllChem as Chem from rdkit.Chem.Draw import IPythonConsole Example: … Continue reading Painting molecules using rdkit and iPython Notebook
Introduction to Virtual Screening
Note: The following is a summary about virtual screening from Leach and Gillet [2007], chapter 8. Virtual screening is the computational analogue of biological screening. Its aim is to filter a set of molecules by scoring and ranking these structures using computational procedures to help researchers take decisions on the tasks being carried out, … Continue reading Introduction to Virtual Screening
Tanimoto Molecular Similarity Experiment
One way to rank and filter molecules from a larger set is to use similarity coefficients. One such way is by using Tanimoto. The experiment below runs similarity tests on a number of molecules using RDKit libraries (http://www.rdkit.org) and Python. Installing RDKit To install RDKit on Ubuntu 14.04 desktop OS, do: sudo apt-get install python-rdkit … Continue reading Tanimoto Molecular Similarity Experiment