Professor Gray's Video Lectures

(540.202) Introduction to Chemical and Biological Process Analysis    Website
(540.414) Computational Protein Structure Prediction and Design    Website



We accept applicants throughout the year on the following broad projects:

Docking of Therapeutic Antibodies: To improve the protein-protein docking algorithm RosettaDock especially for application to therapeutic antibodies, one of the fastest-growing class of new drugs.

Protein Interactions with Solid Surfaces: To work in the general area of protein interactions with solid surfaces, including prediction of the structure of natural proteins interacting with their substrates (e.g. bone morphogenic proteins), computational design of novel protein-surface interactions, and experimental testing of designed proteins. Applicants should have a Ph.D. in a field such as chiical/biomolecular engineering, biophysics, or solid-state/interfacial physics.

We are always interested in applications from well-qualified applicants. Possible projects include protein-protein docking, applications to therapeutic antibodies, protein-surface interactions, and allostery.


For research in computational protein engineering. Junior-level standing in chemical and biomolecular engineering, computer science, biophysics or related field, or serious experience in computer programming.

We sometimes also seek students to assist in molecular biology experiments to validate computational protein designs. Applicants should have some lab or research experience.

Applicants should email a resume and a transcript, including descriptions of proficiency in computer programming or other lab experience.

Professor Gray's Courses

(540.101) Chemical and Biomolecular Engineering in Today's World

Taught Fall 2002

(540.202) Introduction to Chemical and Biological Process Analysis

Taught Fall 2011, Fall 2012, Spring 2014, Spring 2015, Fall 2015

(540.406/606) Molecular Simulations & Multiscale Modeling, taught with German Drazer

Taught Spring 2007, Spring 2008

(540.414/614) Computational Protein Structure Prediction and Design

Taught Spring 2009, Spring 2010, Spring 2012, Spring 2014

(540.416/616) Current Topics in Protein Structure Prediction

Taught Fall 2010, Fall 2012

Miscellaneous Resources

The PyRosetta package for interactive protein structure prediction and design. ROSIE, the Rosetta Online Server that Includes Everyone (includes RosettaAntibody and RosettaDock servers). Allosteric Structures Database CAPRI: Critical Assessment of PRediction of Interactions The Protein Data Bank The GrayLab Wiki