Working Group leader: Marty Ytreberg

Group members: Craig Miller, Tanya Miura, Paul Rowley, Holly Wichman, Brenda Rubenstein, Jagdish Patel, JT Van Leuven, Dharmesh Patel, Ticak Tomislav, Angela Crabtree, LuAnn Scott, Kevin Hutchison, Yesol Sapozhnikov, Jonathan Barnes, Kyle Martin, Laura Steiner, Sierra Beach, Shunji Lee, McKenna Hull, Yunjae Kim, Peik Lund, Hersh Gupta (Brown University)

Originated: October 2014, as the Molecular Modeling Working Group (MoMo)

Description:

We use modeling approaches (e.g., molecular, mathematical, statistical) to understand and predict how amino acid mutations modify the way that proteins fold and bind, and in turn, how these modify organism characteristics.

This working group has grown and changed considerably since its inception. Learn more about the research on the Genotypes to Phenotypes website.

Publications:

Initiating a watch list for Ebola virus antibody escape mutations

Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM (2016) Initiating a watch list for Ebola virus antibody escape mutations. PeerJ 4:e1674.

New Perspectives on Ebola Virus Evolution

Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM, New perspectives on Ebola virus evolution, PLoS One, 11:e0160410 (2016)

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL (2018) Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. PLoS Comput Biol 14(1): e1005974. https://doi.org/10.1371/journal.pcbi.1005974

Fast Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with a Coarse-Grained Model

Patel JS, Ytreberg FM. Fast Calculation of Protein–Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model. Journal of Chemical Theory and Computation 2018 14 (2), 991-997. DOI: 10.1021/acs.jctc.7b00660