Publications



2020


"A dual apolipoprotein C-II mimetictextendashapolipoprotein C-III antagonist peptide lowers plasma triglycerides," A. Wolska, L. Lo, D. O. Sviridov, M. Pourmousa, M. Pryor, S. S. Ghosh, R. Kakkar, M. Davidson, S. Wilson, R. W. Pastor, I. J. Goldberg, D. Basu, S. K. Drake, A. Cougnoux, M. J. Wu, S. B. Neher, L. A. Freeman, J. Tang, M. Amar, M. Devalaraja and A. T. Remaley, Science Translational Medicine, 12 (528) (2020). [DOI] [URL]

"Incorporation of α-methylated amino acids into Apolipoprotein A-I mimetic peptides improves their helicity and cholesterol efflux potential," R. Islam, D. O. Sviridov, S. K. Drake, J. Tunyi, G. Abdoulaeva, L. A. Freeman, R. W. Pastor and A. T. Remaley, Biochemical and Biophysical Research Communications, 526 (2) pp. 349-354 (2020). [URL]

"Characterization of Specific Ion Effects on PI(4,5)P2 Clustering: Molecular Dynamics Simulations and Graph-Theoretic Analysis," K. Han, A. Gericke and R. W. Pastor, J. Phys. Chem. B, 124 (7) pp. 1183-1196 (2020). [DOI] [URL]


2019


"Mannobiose-Grafting Shifts PEI Charge and Biphasic Dependence on pH," S. Basu, R. M. Venable, B. Rice, E. Ogharandukun, J. B. Klauda, R. W. Pastor and P. L. Chandran, Macromolecular Chemistry and Physics, 220 (3) pp. 1800423 (2019). [DOI] [URL]

"Revisiting Volumes of Lipid Components in Bilayers," J. F. Nagle, R. M. Venable, E. Maroclo-Kemmerling, S. Tristram-Nagle, P. E. Harper and R. W. Pastor, The Journal of Physical Chemistry B, 123 (12) pp. 2697-2709 (2019). [DOI] [URL]

"Permeability of membranes in the liquid ordered and liquid disordered phases," A. Ghysels, A. Krämer, R. M. Venable, W. E. Teague, E. Lyman, K. Gawrisch and R. W. Pastor, Nature Communications, 10 (1) pp. 5616 (2019). [URL]

"Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers," S. Park, M. S. Yeom, O. S. Andersen, R. W. Pastor and W. Im, J. Chem. Theory Comput., 15 (11) pp. 6491-6503 (2019). [DOI] [URL]

"Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers," A. Zgorski, R. W. Pastor and E. Lyman, J. Chem. Theory Comput., 15 (11) pp. 6471-6481 (2019). [DOI] [URL]

"Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects," A. Krämer, F. C. Pickard, J. Huang, R. M. Venable, A. C. Simmonett, D. Reith, K. N. Kirschner, R. W. Pastor and B. R. Brooks, J. Chem. Theory Comput., 15 (6) pp. 3854-3867 (2019). [DOI] [URL]

"Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization," M. Mihailescu, M. Sorci, J. Seckute, V. I. Silin, J. Hammer, B. S. Perrin, J. I. Hernandez, N. Smajic, A. Shrestha, K. A. Bogardus, A. I. Greenwood, R. Fu, J. Blazyk, R. W. Pastor, L. K. Nicholson, G. Belfort and M. L. Cotten, J. Am. Chem. Soc., 141 (25) pp. 9837-9853 (2019). [DOI] [URL]

"Molecular Dynamics Simulations of Membrane Permeability," R. Venable, A. Krämer and R. W. Pastor, Chem. Rev., 119 (9) pp. 5954-5997 (2019). [DOI] [URL]


2018


"Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations," A. N. Leonard, A. C. Simmonett, F. C. Pickard, J. Huang, R. M. Venable, J. B. Klauda, B. R. Brooks and R. W. Pastor, Journal of Chemical Theory and Computation, 14 (2) pp. 948-958 (2018). [DOI] [URL]

"Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions," K. Han, R. M. Venable, A.-M. Bryant, C. J. Legacy, R. Shen, H. Li, B. Roux, A. Gericke and R. W. Pastor, The Journal of Physical Chemistry B, 122 (4) pp. 1484-1494 (2018). [DOI] [URL]

"Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model," O. De Vos, R. M. Venable, T. Van Hecke, G. Hummer, R. W. Pastor and A. Ghysels, Journal of Chemical Theory and Computation, 14 (7) pp. 3811-3824 (2018). [DOI] [URL]

"Molecular dynamics simulations of lipid nanodiscs," M. Pourmousa and R. W. Pastor, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1860 (10) pp. 2094 - 2107 (2018). [DOI] [URL]

"Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers," A. N. Leonard, R. W. Pastor and J. B. Klauda, The Journal of Physical Chemistry B, 122 (26) pp. 6744-6754 (2018). [DOI] [URL]

"Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins," M. Pourmousa, H. D. Song, Y. He, J. W. Heinecke, J. P. Segrest and R. W. Pastor, Proceedings of the National Academy of Sciences, 115 (20) pp. 5163-5168 (2018). [DOI] [URL]

"Structural properties of apolipoprotein A-I mimetic peptides that promote ABCA1-dependent cholesterol efflux," R. M. Islam, M. Pourmousa, D. Sviridov, S. M. Gordon, E. B. Neufeld, L. A. Freeman, B. S. Perrin, R. W. Pastor and A. T. Remaley, Scientific Reports, 8 (1) pp. 2956 (2018). [URL]


2017


"Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes," A. H. Beaven, A. J. Sodt, R. W. Pastor, R. E. Koeppe, O. S. Andersen and W. Im, Journal of Chemical Theory and Computation, 13 (10) pp. 5054-5064 (2017). [DOI] [URL]

"Position dependent diffusion tensors in anisotropic media from simulation: oxygen transport in and through membranes," A. Ghysels, R. M. Venable, R. W. Pastor and G. Hummer, Journal of Chemical Theory and Computation, (2017). [DOI]

"Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation," A. H. Beaven, A. M. Maer, A. J. Sodt, H. Rui, R. W. Pastor, O. S. Andersen and W. Im, Biophysical Journal, 112 (6) pp. 1185-1197 (2017). [DOI]

"Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model," A. J. Sodt, A. H. Beaven, O. S. Andersen, W. Im and R. W. Pastor, Biophysical Journal, 112 (6) pp. 1198-1213 (2017). [DOI]

"Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains," S. M. Gordon, M. Pourmousa, M. Sampson, D. Sviridov, R. Islam, B. S. Perrin, G. Kemeh, R. W. Pastor and A. T. Remaley, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1859 (2) pp. 135-145 (2017). [DOI] [URL]

"Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions," R. M. Venable, H. I. Ingólfsson, M. G. Lerner, B. S. Perrin, B. A. Camley, S. J. Marrink, F. L. H. Brown and R. W. Pastor, The Journal of Physical Chemistry B, 121 (15) pp. 3443-3457 (2017). [DOI]


2016


"Nonadditive Compositional Curvature Energetics of Lipid Bilayers," A. J. Sodt, R. M. Venable, E. Lyman and R. W. Pastor, Physical Review Letters, 117 (13) (2016). [DOI]

"Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion," B. S. Perrin Jr. and R. W. Pastor, Biophysical Journal, 111 (6) pp. 1248-1257 (2016). [DOI]

"Simulations of Membrane-disrupting Peptides II: Amp Piscidin 1 Favors Surface Defects Over Pores," B. S. Perrin Jr., R. Fu, M. L. Cotten and R. W. Pastor, Biophysical Journal, 111 (6) pp. 1258-1266 (2016). [DOI]


2015


"Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes," B. A. Camley, M. G. Lerner, R. W. Pastor and F. L. H. Brown, Journal Of Chemical Physics, 143 (24) (2015). [DOI]

"Mechanical properties of lipid bilayers from molecular dynamics simulation," R. M. Venable, F. L. Brown and R. W. Pastor, Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). [DOI] [URL]

"Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin," A. J. Sodt, R. W. Pastor and E. Lyman, Biophysical Journal, 109 (5) pp. 948-955 (2015). [DOI]

"The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length," B. S. Perrin Jr., A. J. Sodt, M. L. Cotten and R. W. Pastor, Journal Of Membrane Biology, 248 (3, SI) pp. 455-467 (2015). [DOI]


2014


"CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature," R. M. Venable, A. J. Sodt, B. Rogaski, H. Rui, E. Hatcher, A. D. MacKerell Jr, R. W. Pastor and J. B. Klauda, Biophysical Journal, 107 pp. 134-145 (2014). [DOI]

"Combining NMR Spectroscopic Measurements and Molecular Dynamics Simulations to Determine the Orientation of Amphipathic Peptides in Lipid Bilayers," B. S. Perrin Jr., R. W. Pastor and M. Cotten, , In Advances in Biological Solid-State NMR: Proteins and Membrane-Active Peptides. pp. 18-35 Royal Society of Chemistry. (2014). [DOI]

"High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion," B. S. Perrin Jr, Y. Tian, R. Fu, C. V. Grant, E. Y. Chekmenev, W. E. Wieczorek, A. E. Dao, R. M. Hayden, C. M. Burzynski, R. M. Venable, M. Sharma, S. J. Opella, R. W. Pastor and M. L. Cotten, Journal of the American Chemical Society, 136 pp. 3321-3712 (2014). [DOI]

"Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape," A. J. Sodt and R. W. Pastor, Biophysical Journal, 106 pp. 1958-1969 (2014). [DOI]

"Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of Pip2 by protein fences in biological membranes," K. I. Lee, W. Im and R. W. Pastor, BMC Biophysics, 7 (1) (2014). [DOI]

"Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations," Z. A. Levine, R. M. Venable, M. C. Watson, M. G. Lerner, J.-E. Shea, R. W. Pastor and F. L. H. Brown, Journal Of The American Chemical Society, 136 (39) pp. 13582-13585 (2014). [DOI]

"The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers," A. J. Sodt, M. L. Sandar, K. Gawrisch, R. W. Pastor and E. Lyman, Journal of the American Chemical Society, 136 (2) pp. 725-732 (2014). [DOI]


2013


"Bending free energy from simulation: Correspondence of planar and inverse hexagonal lipid phases," A. J. Sodt and R. W. Pastor, Biophysical Journal, 104 pp. 2202-2211 (2013). [DOI]

"Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation using NMR Data," R. M. Venable, Y. Luo, K. Gawrisch, B. Roux and R. W. Pastor, Journal of Physical Chemistry B, 117 pp. 10183-10192 (2013). [DOI]

"Theory of Polymer-Nanopore Interactions Refined Using Molecular Dynamics Simulations," A. Balijepalli, J. W. F. Robertson, J. E. Reiner, J. J. Kasianowicz and R. W. Pastor, Journal of the American Chemical Society, 135 pp. 7064-7072 (2013). [DOI]

"Assessing Smectic Liquid-Crystal Continuum Models for Elastic Bilayer Deformations," K. I. Lee, R. W. Pastor, O. S. Andersen and W. Im, Chemistry And Physics Of Lipids, 169 (SI) pp. 19-26 (2013). [DOI]

"Prediction, Refinement and Persistency of Transmembrane Helix Dimers in Lipid Bilayers using Implicit and Explicit Solvent/Lipid Representations: Microsecond Molecular Dynamics Simulations of ErbB1/B2 and EphA1.," L. Zhang, A. J. Sodt, R. M. Venable, R. W. Pastor and M. Buck, Proteins: Structure, Function, and Bioinformatics, 81 (3) pp. 365-376 (2013). [DOI]


2012


"Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers," T. Kim, K. I. Lee, P. Morris, R. W. Pastor, O. S. Andersen and W. Im, Biophysical Journal, 102 pp. 1551-1560 (2012). [DOI]

"The Tension of a Curved Surface from Simulation," A. J. Sodt and R. W. Pastor, Journal of Chemical Physics, 137 pp. 243101-234113 (2012). [DOI]

"Web Interface for Brownian Dynamics Simulation of Ion Transport and Its Applications to Beta-Barrel Pores," K. I. Lee, S. Jo, H. Rui, B. Egwolf, B. Roux, R. W. Pastor and W. Im, Journal of Computational Chemistry, 33 pp. 331-339 (2012). [DOI]

"Structure and Elasticity of Lipid Membranes with Genistein and Daidzein Bioflavinoids Using X-ray Scattering and MD Simulations," M. Raghunathan, Y. Zubovski, R. M. Venable, R. W. Pastor, J. F. Nagle and S. Tristram-Nagle, Journal of Physical Chemistry B, 116 (13) pp. 3928-3927 (2012). [DOI]

"Depth of α-Synuclein in a Bilayer Determined by Fluorescence, Neutron Reflectometry, and Computation," C. M. Pfefferkorn, F. Heinrich, A. J. Sodt, A. S. Maltsev, R. W. Pastor and J. C. Lee, Biophysical Journal, 102 (3) pp. 613-621 (2012). [DOI] [URL]


2011


"Brownian Dynamics Simulations of Ion Transport through VDAC," K. I. Lee, H. Rui, R. W. Pastor and W. Im, Biophysical Journal, 100 pp. 611-619 (2011). [DOI]

"Development of the CHARMM Force Field for Lipids," R. W. Pastor and A. D. MacKerell Jr, Journal of Physical Chemistry Letters, 2 pp. 1526-1532 (2011). [DOI]

"Molecular Dynamics Studies of Ion Permeation in VDAC," H. Rui, K. I. Lee, R. W. Pastor and W. Im, Biophysical Journal, 100 pp. 602-610 (2011). [DOI]

"Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages," U. Golebiewska, J. G. Kay, T. Masters, S. Grinstein, W. Im, R. W. Pastor, S. Scarlata and S. McLaughlin, Molecular Biology of the Cell, 22 (18) pp. 3498-3507 (2011). [DOI] [URL]

"Coarse-Grained Model for PEGylated Lipids: Effect of PEGylation on the Size and Shape of Self-Assembled Structures," H. Lee and R. W. Pastor, Journal of Physical Chemistry B, 115 (24) pp. 7830-7837 (2011). [DOI]


2010


"Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling," R. M. Venable, E. Hatcher, O. Guvench, A. D. MacKerell Jr and R. W. Pastor, Journal of Physical Chemistry B, 114 pp. 12501-12507 (2010). [DOI]

"Single Molecule Diffusion of Membrane-Bound Proteins: Window into Lipid Contacts and Bilayer Dynamics," J. D. Knight, M. G. Lerner, J. G. Marcano-Velazquez, R. W. Pastor and J. J. Falke, Biophysical Journal, 99 pp. 2879-2887 (2010). [DOI]

"Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types," J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O'Connor, D. J. T. C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell Jr and R. W. Pastor, Journal of Physical Chemistry B, 114 (23) pp. 7830-7843 (2010). [DOI]


2009


"A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics," H. Lee, A. H. de Vries, S.-J. Marrink and R. W. Pastor, Journal of Physical Chemistry B, 113 pp. 13186-13194 (2009). [DOI]

"CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses," O. Guvench, E. R. Hatcher, R. M. Venable, R. W. Pastor and A. D. MacKerell Jr, Journal of Chemical Theory and Computation, 5 pp. 2353-2370 (2009). [DOI]

"Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers," R. M. Venable, L. E. Chen and R. W. Pastor, Journal of Physical Chemistry B, 113 pp. 5855-5862 (2009). [DOI]

"Molecular Dynamics Studies of the Conformation of Sorbitol," A. Lerbret, P. Mason, R. Venable, A. Cesaro, M.-L. Saboungi, R. Pastor and J. Brady, Carbohydrate Research, 344 pp. 2229-2235 (2009). [DOI]

"CHARMM: The biomolecular simulation program," B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York and M. Karplus, Journal of Computational Chemistry, 30 (10) pp. 1545-1614 (2009). [DOI]

"Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description," Z. Li, R. M. Venable, L. A. Rogers, D. Murray and R. W. Pastor, Biophysical Journal, 97 (1) pp. 155-163 (2009). [DOI] [URL]


2008


"Additive Empirical Force Field for Hexopyranose Monosaccharides," O. Guvench, S. N. Greene, G. Kamath, J. W. Brady, R. M. Venable, R. W. Pastor and A. D. MacKerell Jr, Journal of Computational Chemistry, 29 pp. 2543-2564 (2008). [DOI]

"Collective and Noncollective Models of NMR Relaxation in Lipid Vesicles and Multilayers," J. B. Klauda, N. V. Eldho, K. Gawrisch, B. R. Brooks and R. W. Pastor, Journal of Physical Chemistry B, 112 pp. 5924-5929 (2008). [DOI]

"Considerations for Lipid Force Field Development," J. B. Klauda, R. M. Venable, A. D. MacKerell Jr. and R. W. Pastor, , In Computational Modeling of Membrane Bilayers Current Topics in Membranes,. 60 pp. 1-48 Elsevier, San Diego. (2008). [DOI] [URL]

"Langevin Network Model of Myosin," B. T. Miller, W. Zheng, R. M. Venable, R. W. Pastor and B. R. Brooks, Journal of Physical Chemistry B, 112 pp. 6274-6281 (2008). [DOI]

"Structure and Dynamics of Helix-0 of the N-BAR Domain in Lipid Micelles and Bilayers," C. Low, U. Weininger, H. Lee, K. Schweimer, I. Neundorf, A. G. Beck-Sickinger, R. W. Pastor and J. Balbach, Biophysical Journal, 95 pp. 4315-4323 (2008). [DOI]

"Molecular Dynamics Studies of Polyethylene Oxide and Polyethylene Glycol: Hydrodynamic Radius and Shape Anisotropy," H. Lee, R. M. Venable, A. D. Mackerell Jr. and R. W. Pastor, Biophysical Journal, 95 (4) pp. 1590-1599 (2008). [DOI]

"Pathways and Populations: Stereoelectronic Insights into the Exocyclic Torsion of 5-(Hydroxymethyl)tetrahydropyran," H. L. Woodcock, B. R. Brooks and R. W. Pastor, Journal of the American Chemical Society, 130 (20) pp. 6345-6347 (2008). [DOI] [URL]

"Rotation of Lipids in Membranes: Molecular Dynamics Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics," J. B. Klauda, M. F. Roberts, A. G. Redfield, B. R. Brooks and R. W. Pastor, Biophysical Journal, 94 (8) pp. 3074-3083 (2008). [DOI] [URL]


2007


"Long-range Lennard-Jones and Electrostatic Interactions in Interfaces: Application of the Isotropic Periodic Sum Method," J. B. Klauda, X. Wu, R. W. Pastor and B. R. Brooks, Journal of Physical Chemistry B, 111 pp. 4393-4400 (2007). [DOI]

"Ab initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2- Ethoxy Tetrahydropyran," H. L. Woodcock, D. Moran, R. W. Pastor, A. D. MacKerell Jr and B. R. Brooks, Biophysical Journal, 93 (1) pp. 1-10 (2007). [DOI]

"Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers," I. Vorobyov, V. M. Anisimov, S. Greene, R. M. Venable, A. Moser, R. W. Pastor and A. D. MacKerell Jr, Journal of Chemical Theory and Computation, 3 (3) pp. 1120-1133 (2007). [DOI] [URL]


2006


"Constant Surface Tension Molecular Dynamics Simulations of Lipid Bilayers with Trehalose," R. M. Venable, A. Skibinsky and R. W. Pastor, Molecular Simulation, 32 pp. 849-855 (2006). [DOI]

"Dynamical Motions of Lipids and a Finite Size Effect in Simulations of Bilayers," J. B. Klauda, B. R. Brooks and R. W. Pastor, Journal of Chemical Physics, 125 pp. 144710-144718 (2006). [DOI]

"Simulation-based Methods for Interpreting X-ray Data from Lipid Bilayers," J. B. Klauda, N. Kučerka, B. R. Brooks, R. W. Pastor and J. F. Nagle, Biophysical Journal, 90 pp. 2796-2807 (2006). [DOI]

"Structural basis of peroxide-mediated changes in human hemoglobin - A novel oxidative pathway," Y. Jia, P. W. Buehler, R. A. Boykins, R. M. Venable and A. I. Alayash, Journal of Biological Chemistry, 282 (7) pp. 4894-4907 (2006). [DOI] [URL]

"Neutralization epitope responsible for the hepatitis B virus subtype-specific protection in chimpanzees," P. Zhang, M.-y. W. Yu, R. Venable, H. J. Alter and J. W.-K. Shih, Proceedings of the National Academy of Sciences, 103 (24) pp. 9214-9219 (2006). [DOI]

"Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme," M. Buck, S. Bouguet-Bonnet, R. W. Pastor and A. D. MacKerell Jr., Biophysical Journal, 90 (4) pp. L36-L38 (2006). [DOI] [URL]


2005


"Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis," J. B. Klauda, R. W. Pastor and B. R. Brooks, Journal of Physical Chemistry B, 109 pp. 16584-15686 (2005). [DOI]

"An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer," J. B. Klauda, B. R. Brooks, A. D. MacKerell Jr, R. M. Venable and R. W. Pastor, Journal of Physical Chemistry B, 109 pp. 5300-5311 (2005). [DOI]

"Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids," P. Lague, B. Roux and R. W. Pastor, Journal of Molecular Biology, 354 pp. 1129-1141 (2005). [DOI]

"The utility of residual dipolar couplings in detecting motion in carbohydrates: application to sucrose," R. M. Venable, F. Delaglio, S. E. Norris and D. I. Freedberg, Carbohydrate Research, 340 pp. 863-874 (2005). [DOI]

"A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose," A. Skibinsky, R. M. Venable and R. W. Pastor, Biophysical Journal, 89 (6) pp. 4111-4121 (2005). [DOI] [URL]

"O-raffinose crosslinked hemoglobin lacks site-specific chemistry in the central cavity: Structural and functional consequences of β93Cys modification," R. A. Boykins, P. W. Buehler, Y. Jia, R. M. Venable and A. I. Alayash, Proteins: Structure, Function, and Bioinformatics, 59 (4) pp. 840-855 (2005). [DOI] [URL]


2004


"Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation," D. I. Freedberg, R. M. Venable, A. Rossi, T. E. Bull and R. W. Pastor, Journal of the American Chemical Society, 126 pp. 10478-10484 (2004). [DOI]

"A Pressure-Based Long-Range Correction for Lennard Jones Interactions In Molecular Dynamics Simulations: Application To Alkanes and Interfaces," P. Lague, R. W. Pastor and B. Brooks, Journal of Physical Chemistry B, 108 (1) pp. 363-368 (2004). [DOI]


2003


"Conformational flexibility of the group B Meningococcal polysaccharide in solution," T. J. Henderson, R. M. Venable and W. Egan, Journal of the American Chemical Society, 125 pp. 2390-2399 (2003). [DOI]

"Sample size considerations for establishing clinical bioequivalence of allergen formulations," R. L. Rabin, J. E. Slater, P. Lachenbruch and R. W. Pastor, , In Proceedings of the 2002 Paul Ehrlich Symposium. (94) pp. 24-33 Druck und Verlagshaus Sperlich, Frankfurt. (2003). [URL]

"Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides," A. M. Dixon, R. M. Venable, G. Widmalm, T. Bull and R. W. Pastor, Biopolymers, 69 (4) pp. 448-460 (2003). [DOI] [URL]


2002


"Molecular dynamics simulations of water wires in a lipid bilayer and water/octane model systems," R. M. Venable and R. W. Pastor, Journal of Chemical Physics, 116 (6) pp. 2663-2664 (2002). [DOI]

"Identification of a binding site for a ganglioside on the receptor binding domain of tetanus toxin," H. A. Louch, E. S. Buczko, M. A. Woody, R. M. Venable and W. F. Vann, Biochemistry, 41 (46) pp. 13644-13652 (2002). [DOI] [URL]

"Micelle-Bound Conformation of a Hairpin-Forming Peptide: A Combined NMR and Molecular Dynamics Study," A. M. Dixon, R. M. Venable, R. W. Pastor and T. Bull, Biopolymers, 65 (4) pp. 284-298 (2002). [DOI]

"Lipid Bilayers, NMR Relaxation, and Computer Simulations," R. W. Pastor, R. M. Venable and S. E. Feller, Accounts of Chemical Research, 35 (6) pp. 438-446 (2002). [DOI] [URL]

"Simulations of Membranes and Other Interfacial Systems Using P21 and Pc Periodic Boundary Conditions," E. A. Dolan, R. M. Venable, R. W. Pastor and B. R. Brooks, Biophysical Journal, 82 (5) pp. 2317-2325 (2002). [DOI]


2001


"Molecular Dynamics Simulations of Octyl Glucoside Micelles: Dynamic Properties," S. Bogusz, R. M. Venable and R. W. Pastor, Journal of Physical Chemistry B, 105 (35) pp. 8312-8321 (2001). [DOI]


2000


"Statistical Considerations in the Establishment of Release Criteria for Allergen Vaccines," J. E. Slater, A. A. Gam, M. D. Solanki, S. H. Burk, F. M. May and R. W. Pastor, , In Proceedings of the 1999 Paul Ehrlich Symposium. pp. 47-56 GIT VERLAG. Darmstadt. (2000). [URL]

"The Determination of Equivalent Doses of Standardized Allergen Vaccines," J. E. Slater and R. W. Pastor, Journal of Allergy and Clinical Immunology, 105 pp. 468-474 (2000). [DOI]

"The Stability of House Dust Mite Allergens in Glycerinated Extracts," L. N. Soldatova, E. J. Paupore, S. H. Burk, R. W. Pastor and J. E. Slater, Journal of Allergy and Clinical Immunology, 105 pp. 482-488 (2000). [DOI]

"ICAM-1 Enhances MHC-peptide Activation of CD8+ T-cells without an Organized Immunological Synapse," J. S. Goldstein, T. Chen, E. Gubina, R. W. Pastor and S. Kozlowski, European Journal of Immunology, 30 (11) pp. 3266-3270 (2000). [DOI]

"Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties," S. Bogusz, R. M. Venable and R. W. Pastor, Journal of Physical Chemistry B, 104 (23) pp. 5462-5470 (2000). [DOI]

"Molecular Dynamics Simulations of Gel (LβI) Phase Lipid Bilayers in Constant Pressure and Constant Surface Tension Ensembles," R. M. Venable, B. R. Brooks and R. W. Pastor, Journal of Chemical Physics, 112 (10) pp. 4822-4832 (2000). [DOI] [URL]


1999


"Constant Surface Tension Simulations of Lipid Bilayers: the Sensitivity of Surface Areas and Compressibilities," S. E. Feller and R. W. Pastor, Journal of Chemical Physics, 111 pp. 1281-1287 (1999). [DOI]

"Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling," T. Rundlof, R. M. Venable, R. W. Pastor, J. Kowalewski and G. Widmalm, Journal of the American Chemical Society, 121 pp. 11847-11854 (1999). [DOI]


1998


"Time Correlation Functions," R. W. Pastor, , In Encyclopedia of Computational Chemistry. pp. 3003-3011 Wiley & Sons, UK. (1998). [DOI]

"Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure," V. Copie, Y. Tomita, S. K. Akiyama, S.-i. Aota, K. M. Yamada, R. M. Venable, R. W. Pastor, S. Krueger and D. A. Torchia, Journal of Molecular Biology, 277 (3) pp. 663-682 (1998). [DOI] [URL]


1997


"Computer simulation of a DPPC phospholipid bilayer: Structural Changes as a Function of Molecular Surface area," S. E. Feller, R. M. Venable and R. W. Pastor, Langmuir, 13 pp. 6555-6561 (1997). [DOI]

"Molecular Dynamics Simulation of Unsaturated Lipid Bilayers at Low Hydration: Parametrization and Comparison with Diffraction Studies," S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell Jr, Biophysical Journal, 73 pp. 2269-2279 (1997). [DOI]

"The Length Scales of Lipid Dynamics and Molecular Dynamics," S. E. Feller and R. W. Pastor, , In Proceedings of the 1997 Pacific Symposium in Biocomputing,. pp. 142-150 World Scientific, Singapore. (1997). [URL]

"Molecular dynamics simulations of an α-(2 → 8)-linked sialic acid tetramer in vacuum and solvent," R. M. Venable, F. Bizik, T. J. Henderson and W. Egan, Journal of Molecular Structure: THEOCHEM, 395-396 pp. 375-388 (1997). [DOI]


1996


"Diffusion Limited First Contact of the Ends of a Polymer: Comparison of Theory and Simulation," R. W. Pastor, R. Zwanzig and A. Szabo, Journal of Chemical Physics, 105 pp. 3878-3882 (1996). [DOI]

"Molecular Dynamics Simulations of Neat Alkanes: the Viscosity Dependence of Rotational Relaxation," Y. Zhang, R. M. Venable and R. W. Pastor, Journal of Physical Chemistry, 100 pp. 2652-2660 (1996). [DOI]

"On Simulating Lipid Bilayers with an Applied Surface Tension: Periodic Boundary Conditions and Undulations," S. E. Feller and R. W. Pastor, Biophysical Journal, 71 pp. 1350-1355 (1996). [DOI]

"Time Scales of Lipid Dynamics and Molecular Dynamics," R. W. Pastor and S. E. Feller, , In Membrane Structure and Dynamics. pp. 3-29 Birkhauser, Boston. (1996). [DOI]

"The Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water," S. E. Feller, R. W. Pastor, A. Rojnuckarin, S. Bogusz and B. R. Brooks, Journal of Physical Chemistry, 100 (42) pp. 17011-17020 (1996). [DOI]


1995


"Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water," Y. Zhang, S. E. Feller, B. R. Brooks and R. W. Pastor, Journal of Chemical Physics, 103 (23) pp. 10252-10266 (1995). [DOI] [URL]

"Computer Simulation of Liquid/Liquid Interfaces. II. Surface Tension-Area Dependence of a Bilayer and Monolayer," S. E. Feller, Y. Zhang and R. W. Pastor, Journal of Chemical Physics, 103 (23) pp. 10267-10276 (1995). [DOI]

"Harmonic analysis of large systems. III. Comparison with molecular dynamics," D. Janezic, R. M. Venable and B. R. Brooks, Journal of Computational Chemistry, 16 (12) pp. 1554-1556 (1995). [DOI] [URL]

"Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation," N. Tjandra, S. E. Feller, R. W. Pastor and A. Bax, Journal of the American Chemical Society, 117 (50) pp. 12562-12566 (1995). [DOI] [URL]

"Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method," S. E. Feller, Y. Zhang, R. W. Pastor and B. R. Brooks, Journal of Chemical Physics, 103 (11) pp. 4613-4621 (1995). [DOI]

"A method for characterizing transition concertedness from polymer dynamics computer simulations," M. L. Brown, R. M. Venable and R. W. Pastor, Biopolymers, 35 (1) pp. 31-46 (1995). [DOI]


1994


"A Comparison of Methods for Computing Transition Rates from Molecular Dynamics Simulation," Y. Zhang and R. W. Pastor, Molecular Simulation, 13 pp. 25-38 (1994). [DOI]

"Techniques and Applications of Langevin Dynamics Simulations," R. W. Pastor, , In The Molecular Dynamics of Liquid Crystals. pp. 85-138 Kluwer Academic Publishers, The Netherlands. (1994). [DOI]

"Molecular Dynamics and Monte Carlo Simulations of Lipid Bilayers," R. W. Pastor, Current Opinion in Structural Biology, 4 (4) pp. 486-492 (1994). [DOI]

"Molecular dynamics simulation and nmr study of a blood group H trisaccharide," G. Widmalm and R. M. Venable, Biopolymers, 34 (8) pp. 1079-1088 (1994). [DOI] [URL]

"Conformational sampling of hydrocarbon and lipid chains in an orienting potential," B. J. Hardy and R. W. Pastor, Journal of Computational Chemistry, 15 (2) pp. 208-226 (1994). [DOI] [URL]


1993


"Molecular and Stochastic Dynamics Simulation of Lipid Membranes," R. W. Pastor and R. M. Venable, , In Computer Simulation of Biomolecular Systems: theoretical and experimental applications. pp. 443-463 ESCOM Science Publishers, Leiden. (1993).

"Theoretical Studies of Relaxation of a Monomeric Subunit of HIV-1 Protease in Water Using Molecular Dynamics," R. M. Venable, B. R. Brooks and F. W. Carson, Proteins, 15 pp. 374-384 (1993). [DOI]

"Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity," R. M. Venable, Y. Zhang, B. J. Hardy and R. W. Pastor, Science, 262 (5131) pp. 223-226 (1993). [DOI]

"Positional time correlation function for one-dimensional systems with barrier crossing: Memory function corrections to the optimized Rouse-Zimm approximation," A. Perico, R. Pratolongo, K. F. Freed, R. W. Pastor and A. Szabo, Journal of Chemical Physics, 98 (1) pp. 564-573 (1993). [DOI]


1992


"A Comparison of Langevin and Molecular Dynamics Simulations: Equilibrium and Dynamics of Ethylene Glycol in Water," G. Widmalm and R. W. Pastor, Journal of the Chemical Society, Faraday Transactions, 88 pp. 1747-1754 (1992). [DOI]

"Langevin Dynamics of a Linear Rotor in a Maier-Saupe Potential: Kramers Turnover of the Flipping Rate," R. W. Pastor and A. Szabo, Journal of Chemical Physics, 97 (7) pp. 5098-5100 (1992). [DOI]

"Comparison Of Langevin And Molecular-Dynamics Simulations - Equilibrium And Dynamics Of Ethylene-Glycol In Water," G. Widmalm and R. W. Pastor, Journal Of The Chemical Society-Faraday Transactions, 88 (13) pp. 1747-1754 (1992). [DOI]

"Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG)," R. M. Venable, G. Widmalm, B. R. Brooks, W. Egan and R. W. Pastor, Biopolymers, 32 (7) pp. 783-794 (1992). [DOI] [URL]

"Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible," G. Barbato, M. Ikura, L. E. Kay, R. W. Pastor and A. Bax, Biochemistry, 31 (23) pp. 5269-5278 (1992). [DOI]

"Langevin Dynamics of Peptides: the Frictional Dependence of Isomerization Rates of N- Acetylalanyl-N'-Methylamide," R. J. Loncharich, B. R. Brooks and R. W. Pastor, Biopolymers, 32 (5) pp. 523-535 (1992). [DOI]


1991


"Analyses of Statistical Errors in Dynamics Simulations," R. W. Pastor, , In Proteins: Structure, Dynamics, Design. pp. 229-233 ESCOM Science Publishers, The Netherlands. (1991).

"Model for the Structure of the Lipid Bilayer," R. W. Pastor, R. M. Venable and M. Karplus, Proceedings of the National Academy of Sciences, 88 pp. 892-896 (1991). [URL]

"Molecular Dynamics Simulation of Methyl Group Relaxation in Water," G. Widmalm, R. W. Pastor and T. Bull, Journal of Chemical Physics, 94 pp. 4097-4098 (1991). [DOI]

"Synexin: Molecular Mechanism of Calcium-Dependent Membrane Fusion and Voltage- Dependent Calcium Channel Activity," H. B. Pollard, E. Rojas, R. W. Pastor, E. M. Rojas, H. R. Guy and A. L. Burns, Annals of the New York Academy of Sciences, 635 pp. 328-351 (1991). [DOI]

"Mean Field Stochastic Boundary Molecular Dynamics Simulation of a Phospholipid in a Membrane," H. D. Loof, S. C. Harvey, J. P. Segrest and R. W. Pastor, Biochemistry, 30 (8) pp. 2099-2113 (1991). [DOI] [URL]


1990


"Determination of Chain Conformations in the Membrane Interior by Brownian Dynamics Simulations," R. W. Pastor, , In Molecular Description of Biological Membrane Components by Computer Aided Conformational Analysis, Volume I. pp. 171-201 CRC Press, Boca Raton. (1990).

"Significant Conformational Changes in an Antigenic Carbohydrate Epitope upon Binding to a Monoclonal Antibody," C. P. Glaudemans, L. Lerner, G. D. Daves Jr, P. Kovac, R. Venable and A. Bax, Biochemistry, 29 pp. 10906-11 (1990). [DOI]


1989


"Anisotropic Bead Models for Molecular Hydrodynamics," R. W. Pastor and R. Zwanzig, Journal of Chemical Physics, 90 pp. 5729-5734 (1989). [DOI]

"Inertial Effects in Butane Stochastic Dynamics," R. W. Pastor and M. Karplus, Journal of Chemical Physics, 91 pp. 211-218 (1989). [DOI]

"Theoretically Determined Three-Dimensional Structures for Amphipathic Segments of the HIV-1 gp41 Envelope Protein," R. M. Venable, R. W. Pastor, B. R. Brooks and F. W. Carson, AIDS Research and Human Retroviruses, 5 pp. 7-21 (1989). [DOI]


1988


"A Simulation Based Model of NMR T1 Relaxation in Lipid Bilayer Vesicles," R. W. Pastor, R. M. Venable, M. Karplus and A. Szabo, Journal of Chemical Physics, 89 pp. 1128-1140 (1988). [DOI]

"Brownian Dynamics Simulation of a Lipid Chain in a Membrane Bilayer," R. W. Pastor, R. M. Venable and M. Karplus, Journal of Chemical Physics, 89 (2) pp. 1112-1127 (1988). [DOI]

"An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms," R. W. Pastor, B. R. Brooks and A. Szabo, Molecular Physics, 65 (6) pp. 1409-1419 (1988). [DOI]

"Frictional Models for Stochastic Simulations of Proteins," R. M. Venable and R. W. Pastor, Biopolymers, 27 (6) pp. 1001-1014 (1988). [DOI]

"Parametrization of the friction constant for stochastic simulations of polymers," R. W. Pastor and M. Karplus, Journal of Physical Chemistry, 92 (9) pp. 2636-2641 (1988). [DOI]


1987


"Local Sequence Patterns of Hydrophobicity and Solvent Accessibility in Soluble Globular Proteins," D. J. Lipman, R. W. Pastor and B. Lee, Biopolymers, 26 pp. 17-26 (1987). [DOI]

"A Theoretically Determined Three-Dimensional Structure for the Repeating Tetrapeptide Unit of the Circumsporozoite Coat Protein of the Malaria Parasite Plasmodium falciparum," B. R. Brooks, R. W. Pastor and F. W. Carson, Proceedings of the National Academy of Sciences, 84 (13) pp. 4470-4474 (1987). [DOI]


1986


"A Recognition Site in Synthetic Helical Oligonucleotides for Monoclonal Anti-Native DNA Autoantibody," D. Stollar, G. Zon and R. W. Pastor, Proceedings of the National Academy of Sciences, 83 pp. 4469-2273 (1986). [DOI]


1978


"Model For Surface Of A Molten-Salt," J. Goodisman and R. W. Pastor, Journal Of Physical Chemistry, 82 (19) pp. 2078-2081 (1978). [DOI]

"Surface-Tension Calculations For Molten-Salts - Critique And Modification Of Fowler Model," R. W. Pastor and J. Goodisman, Journal Of Chemical Physics, 68 (8) pp. 3654-3666 (1978). [DOI]


1976


"Resonance Raman studies of macrocyclic complexes. 1. Structural and electronic effects in synthetic metal(II) porphyrin analogs," W. H. Woodruff, R. W. Pastor and J. C. Dabrowiak, Journal Of The American Chemical Society, 98 (25) pp. 7999-8006 (1976). [DOI]

"Resonance Raman studies of macrocyclic complexes. 2. Antiresonance and selective intensity enhancement in synthetic metal(II) porphyrin analogs," L. A. Nafie, R. W. Pastor, J. C. Dabrowiak and W. H. Woodruff, Journal Of The American Chemical Society, 98 (25) pp. 8007-8014 (1976). [DOI]