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 […]
Reweighting Metadynamics
In my last post I described how to check convergence of metadynamics simulation. However, the 1D free energy surface showed in the previous post is not reweighted and corrected properly because I […]
tICA Metadynamics
Time-lagged independent component analysis is a dimensionality reduction technique which transforms a high dimensional dataset to lower dimensional co-ordinates. It’s philosophy is kind of similar to PCA (principal component analysis). For more […]
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 […]
MD study to understand the effect of T68A/N126Y mutations on CVB3 3C protease
One of the first paper which described the effect of T68A/N126Y double mutations got accepted recently in Molecular Biosystems. The paper entitled “Effect of T68A/N126Y mutations on conformational and ligand binding landscape […]
New manuscript accepted in Journal of Biomolecular Structure & Dynamics
One of our new manuscript which deals with effect of PR20 mutations on flap movement as well as conformational dynamics of apo and bound conformations of HIV-1 Protease is accepted in Journal […]
Our paper on Plasmepsin
One of our recent paper entitled “Flap Dynamics of Plasmepsin Proteases: Proposed Parameters and Molecular Dynamics Insight” is published recently in Molecular Biosystems. This paper describes first ever proposed parameters which will […]
Research Interests
Research Interests.
Publications
Publications.
Welcome to the homepage of Soumendranath Bhakat whose research interest is within the exciting field of biology, chemistry and computational applications. This webpage not only highlights current research interests, publications but also […]
