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Latest posts

  • Analysis of MD trajectory using tSNE

    Before starting anything with tSNE let’s read what is tSNE and how it has been compared with PCA. You can read it here. Several implementations of t-SNE are available here. A great introductory video on tSNE can be found here. The dataset used in this explanation can be accessed here (named combine_times_ca.dcd and corresponding GRO file […]

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  • Jupyter notebook and Matplotlib

    I was thinking to use Jupyter notebook for quite a some time and finally I started using it. Here is a quick installation guide for Linux (Ubuntu). If Python is already installed pip3 install –upgrade pip pip3 install jupyter Also you can install it with Anaconda. Details here  To run notebook  jupyter notebook This will […]

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  • Useful scripts

    Disclaimer: All these scripts were written by Emil Åberg Imagine you have multiple folders with rec.pdbqt and rec.pdb files and have a folder with all the ligands with .pdbqt files. Imagine now you want to dock all the ligands with receptors present in all the folders. You can use a script something like the following […]

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Learn to Explore

Great scientists, artists, entrepreneurs, sports persons are explorers. Following a path defined by the society and incentive structures kills the explorer mindset. Modern science need true explorers.

Make connections

Technologies are build by people. Bringing together a diverse set of people is necessary for substainable technological advancements. Make sure to build connections with people. It matters.

Biology is fascinating. Understanding biological functions at molecular level has significant implications in human disease. I help understanding molecular basis of biological events using physics-based simulations.