Tuesday, July 25, 2017

Lecture 21: Rebecca Alford (Jeff Gray Lab)

A deep-dive into the Rosetta all-atom energy function
Over the past decade, the Rosetta biomolecular modeling suite has informed various biological questions and engineering challenges ranging from folding and docking to the interpretation of low-resolution structural data, design of nanomaterials, and vaccines. Central to Rosetta’s success is the energy function: a set of mathematical models used to approximate the free energy of a macromolecule. In this presentation, Rebecca will describe the concepts and calculations that underlie the Rosetta energy function. I will present the mathematics and origin of the major energy terms (van der Waals, implicit solvation, electrostatics, and hydrogen bonding, and design reference energies), and Rebecca will explain where numerical stability and efficiency limitations have led to modifications of these functions. Applying these concepts, she will explain how to use a Rosetta energy calculation to select and analyze the features of output models. Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membranes, DNA, RNA, and other macromolecules.

Rebecca Alford is a Chemical and Biomolecular Engineering Ph.D. Student in Jeff Gray’s Lab at Johns Hopkins University. Her overall goal is to develop computational tools to investigate biology and disease at the molecular level. As an undergraduate, she created RosettaMP: a suite of tools to investigate membrane protein structures. Currently, she is developing computational models of cell membrane environments toward improving energy functions for structure prediction and design. Rebecca is funded by a Hertz Foundation Fellowship and a National Science Foundation Graduate Research Fellowship.