Let’s Build Something Together
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…
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
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…
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.
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.