Loading...
A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation
A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation
Abstract
In this thesis we develop a molecular modeling toolkit that models the conformation space of proteins and allows easy prototyping of algorithms on the conformation space models, by extending an existing molecular modeling tool. Our toolkit creates a factor graph to represent the conformation space model and links it with an inference framework. This enables execution of statistical inference tasks and implementation of algorithms that work on graphical models. As an application of our toolkit, we study estimating free energy changes after mutations. We show that it is possible to represent molecular dynamics trajectories using graphical models and free energy perturbation calculations can be done efficiently on these models.
Type
campus
article
thesis
article
thesis
Date
2010-01-01