A simple method for faster nonbonded force evaluations. - Min-Yi Shen; Karl F. Freed (J. Comput. Chem., 2005)

A Probabilistic Graphical Model for Ab Initio Folding. - Feng Zhao; Jian Peng 001; Joe DeBartolo; Karl F. Freed; Tobin R. Sosnick; Jinbo Xu (RECOMB, 2009)

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling. - Feng Zhao; Jian Peng 001; Joe DeBartolo; Karl F. Freed; Tobin R. Sosnick; Jinbo Xu (J. Comput. Biol., 2010)

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. - John M. Jumper; Nabil F. Faruk; Karl F. Freed; Tobin R. Sosnick (PLoS Comput. Biol., 2018)

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. - John M. Jumper; Nabil F. Faruk; Karl F. Freed; Tobin R. Sosnick (PLoS Comput. Biol., 2018)