Off-campus UMass Amherst users: To download campus access theses, please use the following link to log into our proxy server with your UMass Amherst user name and password.

Non-UMass Amherst users: Please talk to your librarian about requesting this thesis through interlibrary loan.

Theses that have an embargo placed on them will not be available to anyone until the embargo expires.

Document Type

Campus Access

Degree Program

Electrical & Computer Engineering

Degree Type

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

Year Degree Awarded

2010

Month Degree Awarded

September

Keywords

proteins, free energy, conformation space, graphical models

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.

First Advisor

Ramgopal R. Mettu

Share

COinS