Life in Computational Biology

Tag: molecular dynamics

  • From AlphaFold to Dynamics

    Introducing AlphaFold-SFA, a novel method combining AlphaFold, slow feature analysis (SFA), and metadynamics to accelerate the sampling of rare events like cryptic pocket openings, protein-ligand bindings, and allostery in proteins. This method overcomes limitations of traditional molecular dynamics by using SFA as a dimensionality reduction tool, thus enabling more efficient exploration of protein dynamics and

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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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  • 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 details check here. It is a very recently developed technique which has a lot of promise. tICA can separate slow degrees of freedom

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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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  • Research Interests

    Research Interests.

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  • Publications

    Publications.

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  • Untitled post 2

    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 contains links of several softwares and servers used in the field of computational biology, molecular modelling and drug discovery. My current focus lies

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