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ORCIDJeffery B. Klauda
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2020 – today
- 2022
[i2]Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks:
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules. CoRR abs/2201.04609 (2022)- 2021
- [j7]Mahdi Ghorbani
, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks:
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. J. Comput. Aided Mol. Des. 35(5): 667-677 (2021) - [j6]Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, Yifei Qi, Jeffery B. Klauda, Göran Widmalm, Syma Khalid, Wonpil Im:
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. J. Chem. Inf. Model. 61(2): 831-839 (2021) - [i1]Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks:
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders. CoRR abs/2108.12493 (2021)
2010 – 2019
- 2019
- [j5]Yifei Qi, Jumin Lee, Jeffery B. Klauda, Wonpil Im:
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. J. Comput. Chem. 40(7): 893-899 (2019) - 2014
- [j4]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:
ST-analyzer: A web-based user interface for simulation trajectory analysis. J. Comput. Chem. 35(12): 957-963 (2014) - [j3]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:
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J. Comput. Chem. 35(27): 1997-2004 (2014) - 2013
- [j2]Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im:
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. J. Chem. Inf. Model. 53(8): 2171-2180 (2013)
2000 – 2009
- 2008
- [j1]Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III:
CHARMMing: A New, Flexible Web Portal for CHARMM. J. Chem. Inf. Model. 48(9): 1920-1929 (2008)
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