Category Archives: Protein

Using rsync to make a local copy of RCSB PDB

Why the pause between posts? This post comes after a long pause. The pause hasn’t been because of lack of interest, but mostly because IDRACK has been keeping busy lately. Recent activities included a nearly 4-week long crash course in Bioinformatics (two 90 minute sessions per week) , delivered through Zoom, so was accessed by… Read More »

The Protein Structure Series: Post – VII

The final post in this series has been published as a screen cast on YouTube. The final code used in the video is Disclaimer: Please keep in mind that the research question was phrased in this way to make it easy to understand and develop code to answer it. In the end of the video… Read More »

The Protein Structure Series: Post – VI

In this series so far, we have looked at protein structure data and introduced a bit of python code to analyse it. The code below loads a protein structure and allows the user the extract the protein’s amino acid sequence. In this post we will try to extract more information from the sequence we have… Read More »

The Protein Structure Series: Post – V

From last time In the last post, we moved from explaining the theory of proteins, especially their 3D structures to actually handling the structures with python in the jupyter notebook. If you are new here please have a look at the preceding posts to catch up. In this post, I will assume you have looked… Read More »

The Protein Structure Series: Post – IV

Recap: Just to refresh for myself and all of you, what we have been looking at so far in the Protein Structure Series is understanding protein structures. While many text books already cover a lot of the basic stuff, these posts are especially structured for aspiring researchers who want to start working with protein structures… Read More »

The Protein Structure Series

Having not added content for a while I think its the right time to start putting together a series of articles centered around my area of expertise, namely Protein Structures. In this series of articles I will aim to cover some basic essentials about: Protein Structures. What are they? Why do we need structures? How… Read More »