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
Sitecore with MongoDB Authentication
Securing website data is critical for any business and it is no exception for Sitecore websites. One of the main components for Sitecore is MongoDB which is the core storage for the xDB data. Authentication is the primary way to protect data stored in xDB. This ensures that only authorised users get access. So what … Continue reading Sitecore with MongoDB Authentication
R Simulation – Monty Hall Problem
Suppose you’re on a game show, and you’re given the choice of three doors: Behind one door is a car; behind the others, goats. You pick a door, say No. 1, and the host, who knows what’s behind the doors, opens another door, say No. 3, which has a goat. He then says to you, … Continue reading R Simulation – Monty Hall Problem