R. Venable

发表

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Alexander D. MacKerell, Jeffery B. Klauda, B. Brooks, 2005, The journal of physical chemistry. B.

Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity.

R M Venable, B. J. Hardy, R. Pastor, 1993, Science.

Mannobiose‐Grafting Shifts PEI Charge and Biphasic Dependence on pH

Preethi L. Chandran, Jeffery B. Klauda, R. Pastor, 2019, Macromolecular Chemistry and Physics.

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Alexander D. MacKerell, Jeffery B. Klauda, D. Tobias, 2010, The journal of physical chemistry. B.

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

Alexander D. MacKerell, Huan Rui, Jeffery B. Klauda, 2014, Biophysical journal.

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, Journal of chemical theory and computation.

Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data.

B. Roux, R. Pastor, R. Venable, 2013, The journal of physical chemistry. B.

Theoretical studies of relaxation of a monomeric subunit of HIV‐1 protease in water using molecular dynamics

B. Brooks, R. Venable, F. Carson, 1993, Proteins.

A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose.

R. Pastor, R. Venable, A. Skibinsky, 2005, Biophysical journal.

Chapter 1 Considerations for Lipid Force Field Development

Alexander D. MacKerell, Jeffery B. Klauda, R. Pastor, 2008 .

Mechanical properties of lipid bilayers from molecular dynamics simulation.

R. Pastor, R. Venable, F. Brown, 2015, Chemistry and physics of lipids.

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

Alexander D. MacKerell, R. Pastor, R. Venable, 2008, Biophysical journal.

Molecular Dynamics Simulations of Membrane Permeability.

R. Pastor, R. Venable, A. Krämer, 2019, Chemical reviews.

Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles

B. Brooks, R. Pastor, R. Venable, 2000 .

Membrane permeability of small molecules from unbiased molecular dynamics simulations.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2020, The Journal of chemical physics.

Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose

R. Pastor, R. Venable, A. Skibinsky, 2006 .

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

Benoît Roux, Hui Li, Kyungreem Han, 2018, The journal of physical chemistry. B.

Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling

R. Pastor, R. Venable, G. Widmalm, 1999 .

Design principles of PI(4,5)P2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Soon Ho Kim, K. Han, R. Pastor, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Alexander D. MacKerell, Andrew C. Simmonett, Jeffery B. Klauda, 2020, Journal of chemical theory and computation.

The Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

Jacob J. Kinnun, Frederick A. Heberle, R. Pastor, 2020 .

Molecular dynamics simulations of an α-(2 → 8)-linked sialic acid tetramer in vacuum and solvent

R. Venable, W. Egan, F. Bízik, 1997 .

Separation and quantitation of insulins and related substances in bulk insulin crystals and in injectables by reversed-phase high performance liquid chromatography and the effect of temperature on the separation.

R. Venable, D. J. Smith, J. Collins, 1985, Journal of chromatographic science.

Permeability of membranes in the liquid ordered and liquid disordered phases

R. Pastor, R. Venable, K. Gawrisch, 2019, Nature Communications.

Determination of thermodynamic parameters for the interaction of a lipid-binding peptide and insulin with a reversed-phase column.

W. Hancock, R. Venable, D. Harding, 1986, Journal of chromatography.

Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG)

B. Brooks, R. Pastor, R. Venable, 1992, Biopolymers.

Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides.

Göran Widmalm, R. Pastor, R. Venable, 2003, Biopolymers.

Carbohydrate structure from NMR residual dipolar couplings : Is there a correlation between lactose's anomeric configuration and its three-dimensional structure?

R. Venable, D. Freedberg, Scott E Norris, 2006 .

The utility of residual dipolar couplings in detecting motion in carbohydrates: application to sucrose.

F. Delaglio, R. Venable, D. Freedberg, 2005, Carbohydrate research.

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

Sunhwan Jo, Xi Cheng, Jumin Lee, 2014, J. Comput. Chem..

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.

R. Pastor, R. Venable, A. M. Dixon, 2002, Biopolymers.

Additive empirical force field for hexopyranose monosaccharides

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, J. Comput. Chem..

O‐raffinose crosslinked hemoglobin lacks site‐specific chemistry in the central cavity: Structural and functional consequences of β93Cys modification

P. Buehler, R. Venable, A. Alayash, 2005, Proteins.

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.

R. Pastor, D. Murray, R. Venable, 2009, Biophysical journal.

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for PE, PG, and Ether Lipids

Jeffery B. Klauda, B. Brooks, R. Pastor, 2020 .

Significant conformational changes in an antigenic carbohydrate epitope upon binding to a monoclonal antibody.

A. Bax, R. Venable, P. Kováč, 1990, Biochemistry.

Molecular dynamics studies of the conformation of sorbitol.

J. Brady, M. Saboungi, R. Pastor, 2009, Carbohydrate research.

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2018, Journal of chemical theory and computation.

Revisiting Volumes of Lipid Components in Bilayers.

R. Pastor, R. Venable, J. Nagle, 2019, The journal of physical chemistry. B.

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.

S. Aota, D. Torchia, R. Pastor, 1998, Journal of molecular biology.

High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion

R. Pastor, R. Venable, S. Opella, 2014, Journal of the American Chemical Society.

Conformational flexibility of the group B meningococcal polysaccharide in solution.

R. Venable, W. Egan, T. J. Henderson, 2003, Journal of the American Chemical Society.

Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein.

B. Brooks, R. Pastor, R. Venable, 1989, AIDS research and human retroviruses.

Model for the structure of the lipid bilayer.

R M Venable, M Karplus, M. Karplus, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Lipid bilayers, NMR relaxation, and computer simulations.

R. Pastor, S. Feller, R. Venable, 2002, Accounts of chemical research.

A simulation based model of NMR T1 relaxation in lipid bilayer vesicles

Martin Karplus, Richard W. Pastor, Richard M. Venable, 1988 .

Structural Basis of Peroxide-mediated Changes in Human Hemoglobin

P. Buehler, R. Venable, A. Alayash, 2007, Journal of Biological Chemistry.

The Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle X-ray and Neutron Scattering Data.

Jacob J. Kinnun, Frederick A. Heberle, R. Pastor, 2020, The journal of physical chemistry. B.

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2021, Journal of chemical theory and computation.

Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

Michael G. Lerner, R. Pastor, R. Venable, 2014, Journal of the American Chemical Society.

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Alexander D. MacKerell, Adam Moser, Alexander D MacKerell, 2007, Journal of chemical theory and computation.

Brownian dynamics simulation of a lipid chain in a membrane bilayer

Martin Karplus, Richard W. Pastor, Richard M. Venable, 1988 .

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.

Bernard R Brooks, B. Brooks, R. Pastor, 2002, Biophysical journal.

Harmonic analysis of large systems. III. Comparison with molecular dynamics

Dusanka Janezic, Martin Karplus, Richard M. Venable, 1995, J. Comput. Chem..

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

Matthias Buck, M. Buck, R. Pastor, 2013, Proteins.

Langevin network model of myosin.

Bernard R Brooks, Benjamin T. Miller, Benjamin T Miller, 2008, The journal of physical chemistry. B.

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.

Jeffery B. Klauda, R. Pastor, A. MacKerell, 2023, Journal of chemical theory and computation.

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

G. Hummer, R. Pastor, R. Venable, 2017, Journal of chemical theory and computation.

Computer Simulation of a DPPC Phospholipid Bilayer: Structural Changes as a Function of Molecular Surface Area

Richard W. Pastor, Richard M. Venable, R. Pastor, 1997 .

Surface viscosities of several lipids determined from equilibrium molecular dynamics simulations.

James E. Fitzgerald, R. Pastor, R. Venable, 2023, Biophysical Journal.

Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations.

James E. Fitzgerald, R. Pastor, R. Venable, 2023, Biophysical Journal.

Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.

Helgi I. Ingólfsson, Michael G. Lerner, Brian A. Camley, 2017, The journal of physical chemistry. B.

Structure and elasticity of lipid membranes with genistein and daidzein bioflavinoids using X-ray scattering and MD simulations.

R. Pastor, R. Venable, J. Nagle, 2012, The journal of physical chemistry. B.

Molecular dynamics simulations of water wires in a lipid bilayer and water/octane model systems

R. Pastor, R. Venable, 2002 .

Identification of a binding site for ganglioside on the receptor binding domain of tetanus toxin.

R. Venable, E. Buczko, Richard M Venable, 2002, Biochemistry.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2019, Journal of chemical theory and computation.

Frictional models for stochastic simulations of proteins

R. Pastor, R. Venable, 1988, Biopolymers.

A method for characterizing transition concertedness from polymer dynamics computer simulations

R. Pastor, R. Venable, Michael L. Brown, 1995, Biopolymers.

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.

G. Hummer, R. Pastor, R. Venable, 2018, Journal of chemical theory and computation.

Nonadditive Compositional Curvature Energetics of Lipid Bilayers.

R. Pastor, A. Sodt, R. Venable, 2016, Physical review letters.

Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

R. Pastor, R. Venable, Richard W Pastor, 2009, The journal of physical chemistry. B.

Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids.

Alexander D. MacKerell, Asaminew H. Aytenfisu, R. Pastor, 2021, The journal of physical chemistry. B.

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

Alexander D. MacKerell, R. Pastor, R. Venable, 2008, Biophysical journal.

Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data.

B. Roux, R. Pastor, R. Venable, 2013, The journal of physical chemistry. B.

Atomic-Resolution Three Dimensional Structures and Membrane Locations of Antimicrobial Piscidin 1 and Piscidin 3 in Aligned Lipid Bilayers: A Solid-State NMR and Molecular Dynamics Investigation

R. Pastor, B. Vollmar, R. Venable, 2011 .

Molecular dynamics simulation and nmr study of a blood group H trisaccharide

R. Venable, G. Widmalm, 1994, Biopolymers.

Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate-Ion Interactions and Comparison with CHARMM36.

R. Venable, Zack Jarin, Kyungreem Han, 2024, The journal of physical chemistry. B.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Phillip S. Hudson, Justin A. Lemkul, Andrew C. Simmonett, 2024, The journal of physical chemistry. B.