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Jeffery B. Klauda, Ph.D. - Publications

Affiliations: 
University of Delaware, Newark, DE, United States 
Area:
Statistical, Quantum, and Experimental Thermodynamics
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164 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Niu Y, Chen SJ, Klauda JB. Simulations of naïve and KLA-activated macrophage plasma membrane models. Biochimica Et Biophysica Acta. Biomembranes. 184242. PMID 37866689 DOI: 10.1016/j.bbamem.2023.184242  0.347
2023 Yu Y, Venable RM, Thirman J, Chatterjee P, Kumar A, Pastor RW, Roux B, MacKerell AD, Klauda JB. 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. 19: 2590-2605. PMID 37071552 DOI: 10.1021/acs.jctc.3c00203  0.382
2022 Smith DJ, Klauda JB, Sodt AJ. Simulation Best Practices for Lipid Membranes [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 36204133 DOI: 10.33011/livecoms.1.1.5966  0.4
2022 Allsopp R, Pavlova A, Cline T, Salyapongse AM, Gillilan RE, Di YP, Deslouches B, Klauda JB, Gumbart JC, Tristram-Nagle S. Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation. The Journal of Physical Chemistry. B. PMID 36067064 DOI: 10.1021/acs.jpcb.2c03193  0.317
2022 Fernandes J, Yu Y, Klauda JB. Molecular dynamics simulations of the human ocular lens with age and cataract. Biochimica Et Biophysica Acta. Biomembranes. 184025. PMID 35944665 DOI: 10.1016/j.bbamem.2022.184025  0.327
2022 Karmakar S, Klauda JB. Modeling the membrane binding mechanism of a lipid transport protein Osh4 to single membranes. Biophysical Journal. 121: 1560-1575. PMID 35247338 DOI: 10.1016/j.bpj.2022.03.001  0.343
2021 Hsieh MK, Yu Y, Klauda JB. All-Atom Modeling of Complex Cellular Membranes. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 34962814 DOI: 10.1021/acs.langmuir.1c02084  0.369
2021 Hsieh MK, Klauda JB. Leaflet Asymmetry Modeling in the Lipid Composition of Cytoplasmic Membranes. The Journal of Physical Chemistry. B. PMID 34962410 DOI: 10.1021/acs.jpcb.1c07332  0.302
2021 Yu Y, Klauda JB. Symmetric and Asymmetric Models for the Plasma Membrane: A Simulation Study. The Journal of Physical Chemistry. B. 125: 11418-11431. PMID 34617773 DOI: 10.1021/acs.jpcb.1c04704  0.358
2021 Klauda JB. Considerations of Recent All-Atom Lipid Force Field Development. The Journal of Physical Chemistry. B. 125: 5676-5682. PMID 34048653 DOI: 10.1021/acs.jpcb.1c02417  0.378
2021 Allsopp RJ, Klauda JB. Impact of PIP2 Lipids, Force Field Parameters, and Mutational Analysis on the Binding of the Osh4's α-α Domain. The Journal of Physical Chemistry. B. 125: 5296-5308. PMID 33984230 DOI: 10.1021/acs.jpcb.0c10393  0.314
2021 Feng S, Wang R, Pastor RW, Klauda JB, Im W. Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes. The Journal of Physical Chemistry. B. PMID 33913729 DOI: 10.1021/acs.jpcb.1c01930  0.38
2021 Kuba JO, Yu Y, Klauda JB. Estimating localization of various statins within a POPC bilayer. Chemistry and Physics of Lipids. 236: 105074. PMID 33676920 DOI: 10.1016/j.chemphyslip.2021.105074  0.364
2021 Yu Y, Krämer A, Venable RM, Brooks BR, Klauda JB, Pastor RW. 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. PMID 33620194 DOI: 10.1021/acs.jctc.0c01327  0.304
2020 Krämer A, Ghysels A, Wang E, Venable RM, Klauda JB, Brooks BR, Pastor RW. Membrane permeability of small molecules from unbiased molecular dynamics simulations. The Journal of Chemical Physics. 153: 124107. PMID 33003739 DOI: 10.1063/5.0013429  0.313
2020 Ghorbani M, Wang E, Krämer A, Klauda JB. Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers. The Journal of Chemical Physics. 153: 125101. PMID 33003717 DOI: 10.1063/5.0013430  0.339
2020 Yu Y, Klauda JB. Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids. The Journal of Physical Chemistry. B. PMID 32639155 DOI: 10.1021/Acs.Jpcb.0C04795  0.498
2020 West A, Zoni V, Teague WE, Leonard AN, Vanni S, Gawrisch K, Tristram-Nagle S, Sachs JN, Klauda JB. How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? The Journal of Physical Chemistry. B. PMID 31916765 DOI: 10.1021/Acs.Jpcb.9B08850  0.471
2020 Guros NB, Balijepalli A, Klauda JB. Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT serotonin receptor. Proceedings of the National Academy of Sciences of the United States of America. 117: 405-414. PMID 31871207 DOI: 10.1073/Pnas.1908848117  0.318
2020 Yu Y, Klauda JB. Update of the CHARMM36 United Atom Chain Model for Lipids Biophysical Journal. 118: 88a. DOI: 10.1016/J.Bpj.2019.11.644  0.349
2020 Yu Y, Krämer A, Klauda JB, Pastor RW. Modifying the CHARMM36 Lipid Force Field for LJ-PME Simulations Biophysical Journal. 118: 87a. DOI: 10.1016/J.Bpj.2019.11.643  0.394
2019 Wang E, Klauda JB. Molecular Structure of the Long Periodicity Phase in the Stratum Corneum. Journal of the American Chemical Society. PMID 31547662 DOI: 10.1021/Jacs.9B08995  0.409
2019 Wong S, Eckersley EL, Berger B, Klauda JB. Probing the pH Effects on Sugar Binding to a Polysaccharide Lyase. The Journal of Physical Chemistry. B. PMID 31366199 DOI: 10.1021/Acs.Jpcb.9B04672  0.362
2019 Hughes AV, Patel DS, Widmalm G, Klauda JB, Clifton LA, Im W. Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation. Biophysical Journal. PMID 30850116 DOI: 10.1016/J.Bpj.2019.02.001  0.495
2019 Wang E, Klauda JB. Structure and Permeability of Ceramide Bilayers and Multilayers. The Journal of Physical Chemistry. B. PMID 30795646 DOI: 10.1021/Acs.Jpcb.9B00037  0.439
2019 Monje-Galvan V, Warburton L, Klauda JB. Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers. Methods in Molecular Biology (Clifton, N.J.). 1949: 325-339. PMID 30790265 DOI: 10.1007/978-1-4939-9136-5_22  0.5
2019 Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chemical Reviews. PMID 30785731 DOI: 10.1021/Acs.Chemrev.8B00384  0.492
2019 Leonard AN, Klauda JB, Sukharev S. Isothermal Titration Calorimetry of Be with Phosphatidylserine Models Guides All-Atom Force Field Development for Lipid-Ion Interactions. The Journal of Physical Chemistry. B. PMID 30681857 DOI: 10.1021/Acs.Jpcb.8B11884  0.415
2019 Qi Y, Lee J, Klauda JB, Im W. CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. Journal of Computational Chemistry. 40: 893-899. PMID 30677169 DOI: 10.1002/Jcc.25773  0.455
2019 Wildermuth KD, Monje-Galvan V, Warburton LM, Klauda JB. Effect of membrane lipid packing on stable binding of the ALPS peptide. Journal of Chemical Theory and Computation. PMID 30633866 DOI: 10.1021/Acs.Jctc.8B00945  0.414
2019 Leonard A, Pastor RW, Klauda JB. Parameterization of the Charmm Force Field for Ether Lipids and Model Linear Ethers Biophysical Journal. 116: 506a. DOI: 10.1016/J.Bpj.2018.11.2733  0.347
2019 Khakbaz P, Klauda JB. Ripple and Gel Phases of Saturated Phosphocholine Bilayers Investigated with Simulations Biophysical Journal. 116: 225a. DOI: 10.1016/J.Bpj.2018.11.1239  0.36
2019 Ghorbani M, Wang E, Klauda JB. Calculating Ethanol Permeability of Membranes through Molecular Dynamic Simulations Biophysical Journal. 116: 217a. DOI: 10.1016/J.Bpj.2018.11.1197  0.39
2018 Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. The Journal of Chemical Physics. 149: 220901. PMID 30553261 DOI: 10.1063/1.5055007  0.468
2018 Yu Y, Klauda JB. Modeling inner plasma membrane in planktonic and biofilm modes. The Journal of Chemical Physics. 149: 215102. PMID 30525713 DOI: 10.1063/1.5052629  0.435
2018 Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim SH, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, et al. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Journal of Chemical Theory and Computation. PMID 30525595 DOI: 10.1021/Acs.Jctc.8B01066  0.414
2018 Wang E, Klauda JB. Models for the Stratum Corneum Lipid Matrix: Effects of Ceramide Concentration, Ceramide Hydroxylation, and Free Fatty Acid Protonation. The Journal of Physical Chemistry. B. PMID 30486646 DOI: 10.1021/Acs.Jpcb.8B06188  0.436
2018 Guros NB, Balijepalli A, Klauda JB. The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin. Biophysical Journal. PMID 30287110 DOI: 10.1016/J.Bpj.2018.09.009  0.457
2018 Monje-Galvan V, Klauda JB. Preferred Binding Mechanism of Osh4's ALPS Motif, Insights From Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 30281310 DOI: 10.1021/Acs.Jpcb.8B07067  0.443
2018 Bera I, Klauda JB. Structural Events in a Bacterial Uniporter Leading to Translocation of Glucose to the Cytosol. Journal of Molecular Biology. PMID 29913162 DOI: 10.1016/J.Jmb.2018.06.021  0.304
2018 Leonard AN, Pastor RW, Klauda JB. Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers. The Journal of Physical Chemistry. B. PMID 29870257 DOI: 10.1021/Acs.Jpcb.8B02743  0.441
2018 Khakbaz P, Klauda JB. Investigation of phase transitions of saturated phosphocholine lipid bilayers via molecular dynamics simulations. Biochimica Et Biophysica Acta. PMID 29709614 DOI: 10.1016/J.Bbamem.2018.04.014  0.404
2018 Wang E, Klauda JB. Simulations of Pure Ceramide and Ternary Lipid Mixtures as Simple Interior Stratum Corneum Models. The Journal of Physical Chemistry. B. PMID 29466860 DOI: 10.1021/Acs.Jpcb.8B00348  0.445
2018 Gavrilenko L, Klauda JB. Aggregation of modified hexabenzocoronenes as models for early stage asphaltene self-assembly Molecular Simulation. 44: 992-1003. DOI: 10.1080/08927022.2018.1469752  0.315
2018 Guros NB, Klauda JB, Balijepalli A. Analyzing the Effects of Membrane Lipid Type on Transmembrane Proteins (αHL and 5-HT3) using Molecular Dynamics Simulations Biophysical Journal. 114: 149a. DOI: 10.1016/J.Bpj.2017.11.837  0.423
2018 Feng S, Klauda JB, Im W. Function, Property, and Interaction of Archaeal Lipids: A Molecular Dynamics Simulation Study Biophysical Journal. 114: 459a. DOI: 10.1016/J.Bpj.2017.11.2534  0.427
2018 Khakbaz P, Klauda JB. Probing Plexin A3 Dimerization and the Importance of the Near Membrane Extracellular Residues Biophysical Journal. 114: 423a. DOI: 10.1016/J.Bpj.2017.11.2345  0.323
2018 Lee J, Widmalm G, Klauda JB, Im W. Charmm-GUI Membrane Builder with Glycolipids and Lipopolysaccharides Biophysical Journal. 114: 344a. DOI: 10.1016/J.Bpj.2017.11.1920  0.361
2018 Wang E, Klauda J. Molecular Dynamics Simulations of Stratum Corneum Model Membranes Biophysical Journal. 114: 269a. DOI: 10.1016/J.Bpj.2017.11.1554  0.437
2018 Kern NR, Lee J, Fine-Morris M, Klauda JB, Kuczera K, Fleming P, Im W. CHARMM-GUI Lecture Series on Molecular Modeling and Simulation Biophysical Journal. 114: 184a. DOI: 10.1016/J.Bpj.2017.11.1027  0.361
2018 Guros NB, Balijepalli AK, Klauda JB. The Role of Lipid Interactions in Accurate Simulations of the alpha-hemolysin Transporter Biophysical Journal. DOI: 10.1002/Https://Doi.Org/10.1016/J.Bpj.2018.09.009  0.363
2017 Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW. Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations. Journal of Chemical Theory and Computation. PMID 29268012 DOI: 10.1021/Acs.Jctc.7B00948  0.413
2017 Adams M, Wang E, Zhuang X, Klauda JB. Simulations of Simple Bovine and Homo sapiens Outer Cortex Ocular Lens Membrane Models with a Majority Concentration of Cholesterol. Biochimica Et Biophysica Acta. PMID 29169746 DOI: 10.1016/J.Bbamem.2017.11.010  0.471
2017 Wang E, Klauda JB. Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers. The Journal of Physical Chemistry. B. PMID 29017324 DOI: 10.1021/Acs.Jpcb.7B08967  0.469
2017 Tan Z, Khakbaz P, Chen Y, Lombardo J, Yoon JM, Shanks JV, Klauda JB, Jarboe LR. Engineering Escherichia coli Membrane Phospholipid Head Distribution Improves Tolerance and Production of Biorenewables. Metabolic Engineering. PMID 28867349 DOI: 10.1016/J.Ymben.2017.08.006  0.375
2017 Zhuang X, Ou A, Klauda JB. Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes. The Journal of Chemical Physics. 146: 215103. PMID 28595398 DOI: 10.1063/1.4983655  0.478
2017 Bera I, Klauda JB. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids and Cholesterol. The Journal of Physical Chemistry. B. PMID 28447449 DOI: 10.1021/Acs.Jpcb.7B00359  0.471
2017 Wang E, Klauda JB. An Examination of Mixtures Containing Sphingomyelin and Cholesterol by Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 28399628 DOI: 10.1021/Acs.Jpcb.7B01832  0.478
2017 Monje-Galvan V, Klauda JB. Two sterols, two bilayers: insights on membrane structure from molecular dynamics Molecular Simulation. 43: 1179-1188. DOI: 10.1080/08927022.2017.1353690  0.47
2017 Novikov AA, Semenov AP, Monje-Galvan V, Kuryakov VN, Klauda JB, Anisimov MA. Dual Action of Hydrotropes at the Water/Oil Interface The Journal of Physical Chemistry C. 121: 16423-16431. DOI: 10.1021/Acs.Jpcc.7B05156  0.319
2017 Monje-Galvan V, Klauda JB. Asymmetric Membrane Models for the PM And TGN of Yeast, An All-Atom Molecular Dynamics Study Biophysical Journal. 112: 137a. DOI: 10.1016/J.Bpj.2016.11.761  0.481
2017 Khakbaz P, Klauda J. Simulations Provide Insight into Improving the Tolerance of the E. coli Membrane Biophysical Journal. 112: 83a. DOI: 10.1016/J.Bpj.2016.11.494  0.371
2017 Zhuang X, Ou A, Klauda JB. Simulation of Linoleoyl-Containing Pure Lipid Bilayer and Soybean Plasma Membranes Biophysical Journal. 112: 82a. DOI: 10.1016/J.Bpj.2016.11.486  0.459
2017 Guros NB, Klauda JB. Analyzing the Effects of Lipid Type on the α-Hemolysin Nanopore and 5HT3 Receptor Structure and Gating using Molecular Dynamics Simulations Biophysical Journal. 112: 275a-276a. DOI: 10.1016/J.Bpj.2016.11.1493  0.44
2016 Patel DS, Park S, Wu EL, Yeom MS, Widmalm G, Klauda JB, Im W. Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature. Biophysical Journal. 111: 1987-1999. PMID 27806280 DOI: 10.1016/J.Bpj.2016.09.021  0.414
2016 Boughter CT, Monje-Galvan V, Im W, Klauda JB. Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. The Journal of Physical Chemistry. B. PMID 27771953 DOI: 10.1021/Acs.Jpcb.6B08574  0.462
2016 Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophysical Journal. 111: 1750-1760. PMID 27760361 DOI: 10.1016/J.Bpj.2016.09.001  0.433
2016 Zhuang X, Dávila-Contreras EM, Beaven AH, Im W, Klauda JB. An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. Biochimica Et Biophysica Acta. PMID 27664502 DOI: 10.1016/J.Bbamem.2016.09.016  0.445
2016 Zhuang X, Klauda JB. Modeling structural transitions from the periplasmic-open state of lactose permease and interpretations of spin label experiments. Biochimica Et Biophysica Acta. PMID 27107553 DOI: 10.1016/J.Bbamem.2016.04.008  0.372
2016 Monje-Galvan V, Klauda JB. Peripheral membrane proteins: Tying the knot between experiment and computation. Biochimica Et Biophysica Acta. PMID 26903211 DOI: 10.1016/J.Bbamem.2016.02.018  0.458
2016 Adhikari A, Re S, Nishima W, Ahmed M, Nihonyanagi S, Klauda JB, Sugita Y, Tahara T. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation The Journal of Physical Chemistry C. 120: 23692-23697. DOI: 10.1021/Acs.Jpcc.6B08980  0.337
2016 Khakbaz P, Klauda J. Probing the Ripple Phase of Lipid Bilayers using Molecular Simulations Biophysical Journal. 110: 86a. DOI: 10.1016/J.Bpj.2015.11.524  0.384
2016 Monje-Galvan V, Klauda JB. Lo/Ld Phase Coexistence and Interaction in Model Membranes with IPC Lipids Biophysical Journal. 110: 86a. DOI: 10.1016/J.Bpj.2015.11.523  0.469
2016 Guros NB, Klauda JB. Characterizing Nanopore-Polymer Interactions and Cys-loop Protein Receptor Gating Biophysical Journal. 110: 630a-631a. DOI: 10.1016/J.Bpj.2015.11.3376  0.35
2016 Bera I, Khakbaz P, Klauda JB. PlexinA3 Trans- and Juxtamembrane Dimer Helix Association Biophysical Journal. 110: 324a. DOI: 10.1016/J.Bpj.2015.11.1741  0.384
2016 Zhuang X, Klauda JB. Probing Conformational Changes of Secondary Active Transport Proteins Biophysical Journal. 110: 322a. DOI: 10.1016/J.Bpj.2015.11.1729  0.377
2015 MacDermaid CM, Kashyap HK, DeVane RH, Shinoda W, Klauda JB, Klein ML, Fiorin G. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes. The Journal of Chemical Physics. 143: 243144. PMID 26723629 DOI: 10.1063/1.4937153  0.481
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, ... Klauda JB, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  0.456
2015 Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophysical Journal. 109: 2090-2100. PMID 26588568 DOI: 10.1016/J.Bpj.2015.10.009  0.398
2015 Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical Journal. 109: 2012-2022. PMID 26588561 DOI: 10.1016/J.Bpj.2015.10.008  0.477
2015 Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? Journal of Chemical Theory and Computation. 11: 3466-3477. PMID 26575780 DOI: 10.1021/Acs.Jctc.5B00232  0.5
2015 Monje-Galvan V, Klauda JB. Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties. Biochemistry. 54: 6852-61. PMID 26497753 DOI: 10.1021/Acs.Biochem.5B00718  0.458
2015 Konas RM, Daristotle JL, Harbor NB, Klauda JB. Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations. The Journal of Physical Chemistry. B. PMID 26390264 DOI: 10.1021/Acs.Jpcb.5B06066  0.368
2015 Khakbaz P, Klauda JB. Probing the importance of lipid diversity in cell membranes via molecular simulation. Chemistry and Physics of Lipids. PMID 26260616 DOI: 10.1016/J.Chemphyslip.2015.08.003  0.483
2015 Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods in Molecular Biology (Clifton, N.J.). 1273: 391-406. PMID 25753722 DOI: 10.1007/978-1-4939-2343-4_24  0.456
2015 Kang H, Klauda JB. Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers Molecular Simulation. 41: 948-954. DOI: 10.1080/08927022.2014.926548  0.462
2015 Monje-Galvan V, Klauda JB. Membrane Binding of the Osh4 Curvature-Sensing Peptide Biophysical Journal. 108: 466a. DOI: 10.1016/J.Bpj.2014.11.2547  0.465
2015 Zhuang X, Klauda JB. Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease Biophysical Journal. 108: 466a. DOI: 10.1016/J.Bpj.2014.11.2545  0.361
2015 Boughter CT, Klauda JB. Influence of Cholesterol on Phospholipid Bilayer Dynamics Biophysical Journal. 108: 410a. DOI: 10.1016/J.Bpj.2014.11.2251  0.449
2015 Kang H, Klauda JB. Molecular Dynamics Simulations of Sphingomyelin-Cholesterol Bilayers Biophysical Journal. 108: 410a. DOI: 10.1016/J.Bpj.2014.11.2250  0.495
2015 Khakbaz P, Klauda J. Investigating Lipid Phase Changes from Liquid Crystalline to Ripple to Gel Phases with All-Atom Molecular Dynamics Simulations Biophysical Journal. 108: 410a. DOI: 10.1016/J.Bpj.2014.11.2249  0.399
2015 Konas RM, Daristotle JL, Harbor NB, Klauda JB. How Does Ethanol Affect the Stability of Simple Model Yeast Membranes? Biophysical Journal. 108: 244a. DOI: 10.1016/J.Bpj.2014.11.1350  0.438
2014 Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophysical Journal. 107: 1885-95. PMID 25418169 DOI: 10.1016/J.Bpj.2014.09.007  0.484
2014 Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/Jcc.23702  0.473
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/J.Bpj.2014.05.034  0.402
2014 Zhuang X, Makover JR, Im W, Klauda JB. A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. Biochimica Et Biophysica Acta. 1838: 2520-9. PMID 24953542 DOI: 10.1016/J.Bbamem.2014.06.010  0.461
2014 Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG, Im W. E. coli outer membrane and interactions with OmpLA. Biophysical Journal. 106: 2493-502. PMID 24896129 DOI: 10.1016/J.Bpj.2014.04.024  0.455
2014 Subramanian D, Klauda JB, Collings PJ, Anisimov MA. Mesoscale phenomena in ternary solutions of tertiary butyl alcohol, water, and propylene oxide. The Journal of Physical Chemistry. B. 118: 5994-6006. PMID 24823321 DOI: 10.1021/Jp4125183  0.301
2014 Wu EL, Qi Y, Song KC, Klauda JB, Im W. Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. The Journal of Physical Chemistry. B. 118: 4315-25. PMID 24689790 DOI: 10.1021/Jp500610T  0.443
2014 Jeong JC, Jo S, Wu EL, Qi Y, Monje-Galvan V, Yeom MS, Gorenstein L, Chen F, Klauda JB, Im W. ST-analyzer: a web-based user interface for simulation trajectory analysis. Journal of Computational Chemistry. 35: 957-63. PMID 24638223 DOI: 10.1002/Jcc.23584  0.4
2014 Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 united atom chain model for lipids and surfactants. The Journal of Physical Chemistry. B. 118: 547-56. PMID 24341749 DOI: 10.1021/Jp410344G  0.481
2014 Davila Contreras EM, Beaven AH, Klauda JB, Im W. Characterization of Pure Lipid Bilayers using Molecular Dynamics Simulations Biophysical Journal. 106: 81a. DOI: 10.1016/J.Bpj.2013.11.523  0.482
2014 Zhuang X, Makover J, Klauda JB. Temperature Dependence of Bilayer Structural Properties Studied with Molecular Dynamics Simulations Biophysical Journal. 106: 80a. DOI: 10.1016/J.Bpj.2013.11.518  0.432
2014 Monje-Galvan V, Klauda JB. Molecular Dynamic Studies on Organelle-Specific Yeast Membrane Models and Amphipathic Lipid Packing Sensor Motif Binding Mechanism Biophysical Journal. 106: 710a. DOI: 10.1016/J.Bpj.2013.11.3916  0.502
2014 Wu EL, Fleming PJ, Klauda JB, Fleming KG, Im W. A Molecular Dynamics Simulation Study of Outer Membrane Phospholipase a (OMPLA) Structure and Dynamics in an Asymmetric Lipopolysaccharide Membrane Biophysical Journal. 106: 656a. DOI: 10.1016/J.Bpj.2013.11.3632  0.482
2014 Khakbaz P, Klauda JB. Studying Conformational Changes of Mhp1 using Unbiased All-Atom Molecular Simulations Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2318  0.427
2013 Villanueva DY, Lim JB, Klauda JB. Influence of ester-modified lipids on bilayer structure. Langmuir : the Acs Journal of Surfaces and Colloids. 29: 14196-203. PMID 24156542 DOI: 10.1021/La403919H  0.45
2013 Wu EL, Engström O, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Widmalm G, Im W. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophysical Journal. 105: 1444-55. PMID 24047996 DOI: 10.1016/J.Bpj.2013.08.002  0.413
2013 Cheng X, Jo S, Lee HS, Klauda JB, Im W. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. Journal of Chemical Information and Modeling. 53: 2171-80. PMID 23865552 DOI: 10.1021/Ci4002684  0.375
2013 Lee S, Tran A, Klauda JB. Developing CHARMM-Compatible Lipid Parameters for Ceramides and United Atom Chains Biophysical Journal. 104: 591a. DOI: 10.1016/J.Bpj.2012.11.3285  0.502
2013 Monje V, Kim T, Im W, Klauda JB. Improved Charmm Force Field for Polyunsaturated Fatty Acid Chains, a Study on DAPC Membranes Biophysical Journal. 104: 590a. DOI: 10.1016/J.Bpj.2012.11.3277  0.483
2013 Cheol Jeong J, Jo S, Song K, Cheng X, Sun Lee H, Klauda JB, Im W. Introduction of Membrane Analyzer and Updates of Membrane Builder Biophysical Journal. 104: 335a. DOI: 10.1016/J.Bpj.2012.11.1865  0.438
2012 Rogaski B, Klauda JB. Membrane-binding mechanism of a peripheral membrane protein through microsecond molecular dynamics simulations. Journal of Molecular Biology. 423: 847-61. PMID 22925581 DOI: 10.1016/J.Jmb.2012.08.015  0.455
2012 Klauda JB, Monje V, Kim T, Im W. Improving the CHARMM force field for polyunsaturated fatty acid chains. The Journal of Physical Chemistry. B. 116: 9424-31. PMID 22697583 DOI: 10.1021/Jp304056P  0.447
2012 Ezzeldin HM, Klauda JB, Solares SD. Modeling of the major gas vesicle protein, GvpA: from protein sequence to vesicle wall structure. Journal of Structural Biology. 179: 18-28. PMID 22580065 DOI: 10.1016/J.Jsb.2012.04.015  0.342
2012 Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophysical Journal. 102: 1341-51. PMID 22455917 DOI: 10.1016/J.Bpj.2012.02.009  0.309
2012 Pandit KR, Klauda JB. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. Biochimica Et Biophysica Acta. 1818: 1205-10. PMID 22274566 DOI: 10.1016/J.Bbamem.2012.01.009  0.467
2012 Lim JB, Rogaski B, Klauda JB. Update of the cholesterol force field parameters in CHARMM. The Journal of Physical Chemistry. B. 116: 203-10. PMID 22136112 DOI: 10.1021/Jp207925M  0.412
2012 Pendse PY, Pandit KR, Klauda JB. Atomic-Level Simulations to Probe Conformational Changes of Secondary Active Transport Proteins Biophysical Journal. 102: 623a. DOI: 10.1016/J.Bpj.2011.11.3393  0.357
2012 Rogaski B, Klauda JB. Osh4 Membrane Binding through Molecular Dynamics Biophysical Journal. 102: 494a. DOI: 10.1016/J.Bpj.2011.11.2708  0.455
2011 O'Connor JW, Klauda JB. Lipid membranes with a majority of cholesterol: applications to the ocular lens and aquaporin 0. The Journal of Physical Chemistry. B. 115: 6455-64. PMID 21539340 DOI: 10.1021/Jp108650U  0.436
2011 Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 115: 6157-65. PMID 21513278 DOI: 10.1021/Jp109629V  0.471
2011 Lim JB, Klauda JB. Lipid chain branching at the iso- and anteiso-positions in complex Chlamydia membranes: a molecular dynamics study. Biochimica Et Biophysica Acta. 1808: 323-31. PMID 20692231 DOI: 10.1016/J.Bbamem.2010.07.036  0.48
2011 Bandyopadhyay AA, Klauda JB. Gas hydrate structure and pressure predictions based on an updated fugacity-based model with the PSRK equation of state Industrial and Engineering Chemistry Research. 50: 148-157. DOI: 10.1021/Ie100440S  0.333
2011 Villanueva DY, Lim JB, Klauda JB. Lipid Bilayers of Ester-Modified Lipids Biophysical Journal. 100: 627a. DOI: 10.1016/J.Bpj.2010.12.3607  0.437
2011 Pendse P, Klauda JB. Mechanistic and Thermodynamic Insights into the Transport Cycle of Lactose Permease Biophysical Journal. 100: 545a. DOI: 10.1016/J.Bpj.2010.12.3177  0.386
2011 Pandit K, Klauda J. In Silico Model Escherichia Coli Membranes: Simulating a Lipid with a Cyclopropane Ring Biophysical Journal. 100: 490a. DOI: 10.1016/J.Bpj.2010.12.2872  0.479
2011 Lim JB, Klauda JB. Refining and Testing CHARMM Lipid Parameters for Biologically Important Membranes Biophysical Journal. 100: 490a. DOI: 10.1016/J.Bpj.2010.12.2871  0.506
2011 Rogaski B, Klauda JB. Phospholipid Binding and Membrane Attachment of the Osh4 Protein Biophysical Journal. 100: 395a. DOI: 10.1016/J.Bpj.2010.12.2347  0.432
2011 Noon MS, Lim JB, MacKerell AD, Klauda J. Structure Prediction and Simulations of the Major Outer Membrane Protein of Chlamydia Biophysical Journal. 100: 321a. DOI: 10.1016/J.Bpj.2010.12.1953  0.416
2010 Rogaski B, Lim JB, Klauda JB. Sterol binding and membrane lipid attachment to the Osh4 protein of yeast. The Journal of Physical Chemistry. B. 114: 13562-73. PMID 20925360 DOI: 10.1021/Jp106890E  0.42
2010 Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/Jp108166K  0.442
2010 Pendse PY, Brooks BR, Klauda JB. Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. Journal of Molecular Biology. 404: 506-21. PMID 20875429 DOI: 10.1016/J.Jmb.2010.09.045  0.398
2010 Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The Journal of Physical Chemistry. B. 114: 7830-43. PMID 20496934 DOI: 10.1021/Jp101759Q  0.506
2010 Pendse PY, Klauda JB. Atomistic Model For the Outward-Facing State of Lactose Permease and Quantification of Ligand Binding Biophysical Journal. 98: 54a. DOI: 10.1016/J.Bpj.2009.12.310  0.422
2010 Klauda JB, Venable RM, Pastor RW. A Modified Lipid Force Field for Charmm: Development and Application to Single-Celled Organism Membranes Biophysical Journal. 98: 282a. DOI: 10.1016/J.Bpj.2009.12.1542  0.512
2010 Rogaski B, Klauda JB. Binding of A Natural Sterol to the Osh4 Protein of Yeast and Membrane Attachment Biophysical Journal. 98: 241a. DOI: 10.1016/J.Bpj.2009.12.1307  0.478
2009 Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical Journal. 97: 50-8. PMID 19580743 DOI: 10.1016/J.Bpj.2009.04.013  0.46
2009 Singh RP, Brooks BR, Klauda JB. Binding and release of cholesterol in the Osh4 protein of yeast. Proteins. 75: 468-77. PMID 18937371 DOI: 10.1002/Prot.22263  0.369
2009 Pendse PY, Brooks BR, Klauda JB. An Atomic-level Model for the Periplasmic Open State of Lactose Permease Biophysical Journal. 96: 430a. DOI: 10.1016/J.Bpj.2008.12.2201  0.443
2008 Klauda JB, Brooks BR. CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. Journal of Chemical Theory and Computation. 4: 107-15. PMID 26619984 DOI: 10.1021/Ct700191V  0.393
2008 Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL. CHARMMing: a new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling. 48: 1920-9. PMID 18698840 DOI: 10.1021/Ci800133B  0.325
2008 Klauda JB, Roberts MF, Redfield AG, Brooks BR, Pastor RW. Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics. Biophysical Journal. 94: 3074-83. PMID 18192349 DOI: 10.1529/Biophysj.107.121806  0.416
2008 Klauda JB, Eldho NV, Gawrisch K, Brooks BR, Pastor RW. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. The Journal of Physical Chemistry. B. 112: 5924-9. PMID 18179193 DOI: 10.1021/Jp075641W  0.43
2008 Klauda JB, Venable RM, MacKerell AD, Pastor RW. Chapter 1 Considerations for Lipid Force Field Development Current Topics in Membranes. 60: 1-48. DOI: 10.1016/S1063-5823(08)00001-X  0.427
2007 Klauda JB, Wu X, Pastor RW, Brooks BR. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. The Journal of Physical Chemistry. B. 111: 4393-400. PMID 17425357 DOI: 10.1021/Jp068767M  0.375
2007 Klauda JB, Brooks BR. Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. Journal of Molecular Biology. 367: 1523-34. PMID 17320103 DOI: 10.1016/J.Jmb.2007.02.001  0.346
2006 Klauda JB, Brooks BR, Pastor RW. Dynamical motions of lipids and a finite size effect in simulations of bilayers. The Journal of Chemical Physics. 125: 144710. PMID 17042634 DOI: 10.1063/1.2354486  0.456
2006 Klauda JB, Kucerka N, Brooks BR, Pastor RW, Nagle JF. Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophysical Journal. 90: 2796-807. PMID 16443652 DOI: 10.1529/Biophysj.105.075697  0.453
2005 Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. The Journal of Physical Chemistry. B. 109: 5300-11. PMID 16863197 DOI: 10.1021/Jp0468096  0.417
2005 Arora G, Klauda JB, Sandler SI. A comparative study of nitrogen physisorption on different C 70 crystal structures using an ab initio based potential Journal of Physical Chemistry B. 109: 17267-17273. PMID 16853204 DOI: 10.1021/Jp050590T  0.666
2005 Klauda JB, Pastor RW, Brooks BR. Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. The Journal of Physical Chemistry. B. 109: 15684-6. PMID 16852989 DOI: 10.1021/Jp0527608  0.354
2005 Jiang J, Klauda JB, Sandler SI. Hierarchical modeling N2 adsorption on the surface of and within a C60 crystal: from quantum mechanics to molecular simulation. The Journal of Physical Chemistry. B. 109: 4731-7. PMID 16851555 DOI: 10.1021/Jp0479567  0.505
2005 Klauda JB, Sandler SI. Global distribution of methane hydrate in ocean sediment Energy and Fuels. 19: 459-470. DOI: 10.1021/Ef049798O  0.479
2005 Klauda JB, Brooks BR, Pastor RW. Structure and dynamics of lipid membranes: How can simulations aid experiments? Aiche Annual Meeting, Conference Proceedings. 10460.  0.365
2004 Jiang J, Klauda JB, Sandier SI. Hierarchical modeling O2 and N2 adsorption in C 168 schwarzite: From quantum mechanics to molecular simulation Journal of Physical Chemistry B. 108: 9852-9860. DOI: 10.1021/Jp0379087  0.357
2004 Klauda JB, Jiang J, Sandler SI. An ab initio study on the effect of carbon surface curvature and ring structure on N2(O2) - Carbon intermodular potentials Journal of Physical Chemistry B. 108: 9842-9851. DOI: 10.1021/Jp037897H  0.525
2004 Klauda JB, Garrison SL, Jiang J, Arora G, Sandler SI. HM-IE: Quantum chemical hybrid methods for calculating interaction energies Journal of Physical Chemistry A. 108: 107-112. DOI: 10.1021/Jp035639E  0.725
2003 Jiang JW, Klauda JB, Sandler SI. Monte Carlo simulation of O2 and N2 adsorption in nanoporous carbon (C168 Schwarzite) Langmuir. 19: 3512-3518. DOI: 10.1021/La020319S  0.519
2003 Klauda JB, Sandler SI. Predictions of gas hydrate phase equilibria and amounts in natural sediment porous media Marine and Petroleum Geology. 20: 459-470. DOI: 10.1016/S0264-8172(03)00064-3  0.471
2003 Klauda JB, Sandler SI. Phase behavior of clathrate hydrates: A model for single and multiple gas component hydrates Chemical Engineering Science. 58: 27-41. DOI: 10.1016/S0009-2509(02)00435-9  0.506
2002 Klauda JB, Sandler SI. Ab initio intermolecular potentials for gas hydrates and their predictions Journal of Physical Chemistry B. 106: 5722-5732. DOI: 10.1021/Jp0135914  0.522
2001 Klauda JB, Sandler SI. Modeling gas hydrate phase equilibria in laboratory and natural porous media Industrial and Engineering Chemistry Research. 40: 4197-4208. DOI: 10.1021/Ie000961M  0.514
2000 Klauda JB, Sandler SI. A fugacity model for gas hydrate phase equilibria Industrial and Engineering Chemistry Research. 39: 3377-3386. DOI: 10.1021/Ie000322B  0.455
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