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Access Type

Campus Access

Document Type


Degree Program

Electrical & Computer Engineering

Degree Type

Master of Science in Electrical and Computer Engineering (M.S.E.C.E.)

Year Degree Awarded


Month Degree Awarded



proteins, free energy, conformation space, graphical models


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.


First Advisor

Ramgopal R. Mettu