Jeffery B Klauda

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 54

Top Topics

Pseudomonas Aeruginosa

Molecular Dynamics

Top Venues

The journal of physical chemistry. B

The Journal of chemical physics

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Joshua Lucker, Michael Kio, Jeffery B Klauda
Expanding the CHARMM36 United Atom Chain Model for the Inclusion of Sphingolipids. The journal of physical chemistry. B 128 (18) (2024)
Joshua Lucker, Michael Kio, Jeffery B Klauda
Expanding the CHARMM36 United Atom Chain Model for the Inclusion of Sphingolipids. The journal of physical chemistry. B (2024)
Tejaswi Tammareddy, Walid Keyrouz, Ram D Sriram, Harish C Pant, Antonio Cardone, Jeffery B Klauda
Investigation of the Effect of Peptide p5 Targeting CDK5-p25 Hyperactivity on Munc18-1 (P67) Regulating Neuronal Exocytosis Using Molecular Simulations. Biochemistry 63 (14) (2024)
Jessica Bodosa, Jeffery B Klauda
Metadynamics Study of Lipid-Mediated Antibacterial Toxin Binding to the EmrE Multiefflux Protein. The journal of physical chemistry. B (2024)
Tejaswi Tammareddy, Walid Keyrouz, Ram D Sriram, Harish C Pant, Antonio Cardone, Jeffery B Klauda
Investigation of the Effect of Peptide p5 Targeting CDK5-p25 Hyperactivity on Munc18-1 (P67) Regulating Neuronal Exocytosis Using Molecular Simulations. Biochemistry (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
Tejaswi Tammareddy, Walid Keyrouz, Ram D Sriram, Harish C Pant, Antonio Cardone, Jeffery B Klauda
Investigation of the Effect of Peptide p5 Targeting CDK5-p25 Hyperactivity on Munc18-1 (P67) Regulating Neuronal Exocytosis Using Molecular Simulations. Biochemistry 63 (14) (2024)
Min-Kang Hsieh, Jeffery B Klauda
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. The journal of physical chemistry. B 128 (1) (2023)
Min-Kang Hsieh, Jeffery B Klauda
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. The journal of physical chemistry. B (2023)
Yalun Yu, Richard M Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W Pastor, Benoı T Roux, Alexander D MacKerell, Jeffery B Klauda
Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids. Journal of chemical theory and computation (2023)
Min-Kang Hsieh, Jeffery B Klauda
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. The journal of physical chemistry. B 128 (1) (2023)
Min-Kang Hsieh, Jeffery B Klauda
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. The journal of physical chemistry. B 128 (1) (2023)
Mahdi Ghorbani, Bernard R Brooks, Jeffery B Klauda
Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics. The journal of physical chemistry. B (2023)
Min-Kang Hsieh, Jeffery B Klauda
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. The journal of physical chemistry. B 128 (1) (2023)
Tejaswi Tammareddy, Walid Keyrouz, Ram D Sriram, Harish C Pant, Antonio Cardone, Jeffery B Klauda
Computational Study of the Allosteric Effects of p5 on CDK5-p25 Hyperactivity as Alternative Inhibitory Mechanisms in Neurodegeneration. The journal of physical chemistry. B 126 (27) (2022)
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. The Journal of chemical physics 156 (18) (2022)
Robert Allsopp, Anna Pavlova, Tyler Cline, Aria M Salyapongse, Richard E Gillilan, Yuan-Pu Peter Di, Berthony Deslouches, Jeffery B Klauda, James C Gumbart, Stephanie A Tristram-Nagle
Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation. The journal of physical chemistry. B 126 (36) (2022)
Min-Kang Hsieh, Yalun Yu, Jeffery B Klauda
All-Atom Modeling of Complex Cellular Membranes. Langmuir : the ACS journal of surfaces and colloids 38 (1) (2021)
Yiding Yuan, Yalun Yu, Jeffery B Klauda
Simulations of Diabetic and Non-Diabetic Peripheral Nerve Myelin Lipid Bilayers. The journal of physical chemistry. B 125 (23) (2021)
Mahdi Ghorbani, Samarjeet Prasad, Jeffery B Klauda, Bernard R Brooks
Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders. The Journal of chemical physics 155 (19) (2021)
Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, John Z H Zhang, Jeffery B Klauda, Göran Widmalm, Syma Khalid, Wonpil Im
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. Journal of chemical information and modeling 61 (2) (2021)
Jeffery B Klauda
Virtual Issue on Docking. The journal of physical chemistry. B 125 (21) (2021)
Jeffery B Klauda
Considerations of Recent All-Atom Lipid Force Field Development. The journal of physical chemistry. B 125 (22) (2021)
Yalun Yu, Andreas Krämer, Richard M Venable, Bernard R Brooks, Jeffery B Klauda, Richard W Pastor
CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. Journal of chemical theory and computation 17 (3) (2021)
Min-Kang Hsieh, Jeffery B Klauda
Leaflet Asymmetry Modeling in the Lipid Composition of Escherichia coli Cytoplasmic Membranes. The journal of physical chemistry. B 126 (1) (2021)
Yalun Yu, Jeffery B Klauda
Symmetric and Asymmetric Models for the Arabidopsis thaliana Plasma Membrane: A Simulation Study. The journal of physical chemistry. B 125 (41) (2021)
Mahdi Ghorbani, Eric Wang, Andreas Krämer, Jeffery B Klauda
Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers. The Journal of chemical physics 153 (12) (2021)
Yalun Yu, Andreas Krämer, Richard M Venable, Andrew C Simmonett, Alexander D MacKerell, Jeffery B Klauda, Richard W Pastor, Bernard R Brooks
Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. Journal of chemical theory and computation 17 (3) (2021)
Robert J Allsopp, Jeffery B Klauda
Impact of PIP2 Lipids, Force Field Parameters, and Mutational Analysis on the Binding of the Osh4's α6-α7 Domain. The journal of physical chemistry. B 125 (20) (2021)
Shasha Feng, Ruixing Wang, Richard W Pastor, Jeffery B Klauda, Wonpil Im
Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes. The journal of physical chemistry. B 125 (18) (2021)
Mahdi Ghorbani, Bernard R Brooks, Jeffery B Klauda
Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. The journal of physical chemistry. B 124 (45) (2020)
Mahdi Ghorbani, Bernard R Brooks, Jeffery B Klauda
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2. bioRxiv : the preprint server for biology (2020)
Ana West, Valeria Zoni, Walter E Teague, Alison N Leonard, Stefano Vanni, Klaus Gawrisch, Stephanie A Tristram-Nagle, Jonathan N Sachs, Jeffery B Klauda
How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? The journal of physical chemistry. B 124 (5) (2020)
Andreas Krämer, An Ghysels, Eric Wang, Richard M Venable, Jeffery B Klauda, Bernard R Brooks, Richard W Pastor
Membrane permeability of small molecules from unbiased molecular dynamics simulations. The Journal of chemical physics 153 (12) (2020)
Yalun Yu, Jeffery B Klauda
Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids. The journal of physical chemistry. B 124 (31) (2020)
Alison N Leonard, Eric Wang, Viviana Monje-Galvan, Jeffery B Klauda
Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chemical reviews 119 (9) (2019)
Sook Wong, Evan L Eckersley, Bryan Berger, Jeffery B Klauda
Probing the pH Effects on Sugar Binding to a Polysaccharide Lyase. The journal of physical chemistry. B 123 (33) (2019)
Yalun Yu, Jeffery B Klauda
Modeling Pseudomonas aeruginosa inner plasma membrane in planktonic and biofilm modes. The Journal of chemical physics 149 (21) (2019)
Kyle D Wildermuth, Viviana Monje-Galvan, Linnea M Warburton, Jeffery B Klauda
Effect of Membrane Lipid Packing on Stable Binding of the ALPS Peptide. Journal of chemical theory and computation 15 (2) (2019)
Alison N Leonard, Jeffery B Klauda, Sergei Sukharev
Isothermal Titration Calorimetry of Be2+ with Phosphatidylserine Models Guides All-Atom Force-Field Development for Lipid-Ion Interactions. The journal of physical chemistry. B 123 (7) (2019)
Jeffery B Klauda
Perspective: Computational modeling of accurate cellular membranes with molecular resolution. The Journal of chemical physics 149 (22) (2019)
Nicholas B Guros, Son T Le, Siyuan Zhang, Brent A Sperling, Jeffery B Klauda, Curt A Richter, Arvind Balijepalli
Reproducible Performance Improvements to Monolayer MoS2 Transistors through Exposed Material Forming Gas Annealing. ACS applied materials & interfaces 11 (18) (2019)
Nicholas B Guros, Arvind Balijepalli, Jeffery B Klauda
Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT3A serotonin receptor. Proceedings of the National Academy of Sciences of the United States of America 117 (1) (2019)
Eric Wang, Jeffery B Klauda
Structure and Permeability of Ceramide Bilayers and Multilayers. The journal of physical chemistry. B 123 (11) (2019)
Eric Wang, Jeffery B Klauda
Molecular Structure of the Long Periodicity Phase in the Stratum Corneum. Journal of the American Chemical Society 141 (42) (2019)
Alison N Leonard, Andrew C Simmonett, Frank C Pickard, Jing Huang, Richard M Venable, Jeffery B Klauda, Bernard R Brooks, Richard W Pastor
Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations. Journal of chemical theory and computation 14 (2) (2018)
Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst, Yuriy A Knirel, John Z H Zhang, Sunhwan Jo, Jeffery B Klauda, Göran Widmalm, Wonpil Im
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Journal of chemical theory and computation 15 (1) (2018)
Eric Wang, Jeffery B Klauda
Simulations of Pure Ceramide and Ternary Lipid Mixtures as Simple Interior Stratum Corneum Models. The journal of physical chemistry. B 122 (10) (2018)
Alison N Leonard, Richard W Pastor, Jeffery B Klauda
Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers. The journal of physical chemistry. B 122 (26) (2018)
Viviana Monje-Galvan, Jeffery B Klauda
Preferred Binding Mechanism of Osh4's Amphipathic Lipid-Packing Sensor Motif, Insights from Molecular Dynamics. The journal of physical chemistry. B 122 (42) (2018)
Eric Wang, Jeffery B Klauda
Models for the Stratum Corneum Lipid Matrix: Effects of Ceramide Concentration, Ceramide Hydroxylation, and Free Fatty Acid Protonation. The journal of physical chemistry. B 122 (50) (2018)
Eric Wang, Jeffery B Klauda
Examination of Mixtures Containing Sphingomyelin and Cholesterol by Molecular Dynamics Simulations. The journal of physical chemistry. B 121 (18) (2017)
Indrani Bera, Jeffery B Klauda
Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. The journal of physical chemistry. B 121 (20) (2017)
Eric Wang, Jeffery B Klauda
Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers. The journal of physical chemistry. B 121 (43) (2017)