Life in Computational Biology

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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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  • Parameter for zinc centre proteins

    Parametrization of metallo-proteins always been a challenging problem during the set-up of classical molecular dynamics simulation. This tutorial will describe a short-cut way to set up and Zinc (Zn2+) co-ordinated metallo-protein where Zinc stays in co-ordination with two histidines (HID) and one glutamate as described in the following figure (Figure 1). Note: All the waters…

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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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