Category: Uncategorized
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Predicting kinetics of aromatic side-chain flipping using Markov State Modelling
Aromatic side-chain flipping acts a probe to understand conformational dynamics of biomolecules. In this post, we will see how to predict transition kinetics associated with different side-chain rotameric conformations using Markov State Modelling (MSM). MSM allows one to predict kinetics and equilibrium population associated with conformational dynamics. In this post we will use BACE1 as…
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Train, test and split dataset from MD
Here I will show how to preprocess the time-series data from MD simulation using Sklearn’s train_test_split module
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Read COLVAR file using pandas and formatting
Sometimes it is convenient to read the COLVAR file (Plumed output) using pandas as it can act as a first step for machine learning based data analysis e.g. time-series forecasting, clustering, dimensionality reduction etc. You need to remove the #! FIELDS part from the header. The modified header looks like time meanfree_sin_chi1_75 meanfree_sin_chi1_76 meanfree_sin_chi1_77 meanfree_sin_chi1_78…
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Possible new idea with tSNE
Dimensionality reduction is in the hurt of molecular dynamics simulations keeping in mind its importance in reducing the high-dimension data produced during molecular dynamics simulations. It also found application in building Markov State Models and also used as CVs to drive enhanced sampling simulations. Several dimensionality reduction techniques have been used over the years such…
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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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Modelling of ZIKA proteases
Disclaimer: This blog is made public in order to inspire a new generation of enthusiastic people to start working on this neglected disease as soon as possible. I was doing some side-project especially with flaviviruses and the drug discovery targeting flavivirus proteases. That’s why ZIKA break into the scene of my research as ZIKA is…
Life in Computational Biology 