GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2022)

A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge - Mahdi Ghorbani; Phillip S. Hudson; Michael R. Jones; Félix Aviat; Rubén Meana-Pañeda; Jeffery B. Klauda; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2021)

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides - Ya Gao; Jumin Lee; Iain Peter Shand Smith; Hwayoung Lee; Seonghoon Kim; Yifei Qi; Jeffery B. Klauda; Göran Widmalm; Syma Khalid; Wonpil Im (J. Chem. Inf. Model., 2021)

Variational embedding of protein folding simulations using gaussian mixture variational autoencoders - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2021)

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems - Yifei Qi; Jumin Lee; Jeffery B. Klauda; Wonpil Im (J. Comput. Chem., 2019)

ST-analyzer: A web-based user interface for simulation trajectory analysis - Jong Cheol Jeong; Sunhwan Jo; Emilia L. Wu; Yifei Qi; Viviana Monje-Galvan; Min Sun Yeom; Lev Gorenstein; Feng Chen; Jeffery B. Klauda; Wonpil Im (J. Comput. Chem., 2014)

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations - Emilia L. Wu; Xi Cheng; Sunhwan Jo; Huan Rui; Kevin C. Song; Eder M. Dávila-Contreras; Yifei Qi; Jumin Lee; Viviana Monje-Galvan; Richard M. Venable; Jeffery B. Klauda; Wonpil Im (J. Comput. Chem., 2014)

CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems - Xi Cheng; Sunhwan Jo; Hui Sun Lee; Jeffery B. Klauda; Wonpil Im (J. Chem. Inf. Model., 2013)

CHARMMing: A New, Flexible Web Portal for CHARMM - Benjamin T. Miller; Rishi P. Singh; Jeffery B. Klauda; Milan Hodoscek; Bernard R. Brooks; H. Lee Woodcock III (J. Chem. Inf. Model., 2008)