Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)
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journal
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September 2008 |
Insights into the Molecular Mechanism of Membrane Fusion from Simulation: Evidence for the Association of Splayed Tails
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October 2003 |
Digging a hole: Scaled-particle theory and cavity solvation in organic solvents
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November 2008 |
NAMD2: Greater Scalability for Parallel Molecular Dynamics
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journal
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May 1999 |
Conformational change and protein–protein interactions of the fusion protein of Semliki Forest virus
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journal
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January 2004 |
Investigation of Finite System-Size Effects in Molecular Dynamics Simulations of Lipid Bilayers
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journal
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November 2006 |
Capturing a Flavivirus Pre-Fusion Intermediate
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journal
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November 2009 |
Chapter 4 Hydration, Curvature, and Bending Elasticity of Phospholipid Monolayers
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book
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January 1997 |
Interaction of the Dengue Virus Fusion Peptide with Membranes Assessed by NMR: The Essential Role of the Envelope Protein Trp101 for Membrane Fusion
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journal
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September 2009 |
A New Coarse-Grained Force Field for Membrane–Peptide Simulations
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journal
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October 2011 |
Conformational Changes of the Flavivirus E Glycoprotein
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journal
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September 2004 |
Potential of Mean Force and p K a Profile Calculation for a Lipid Membrane-Exposed Arginine Side Chain
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journal
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August 2008 |
Coupling Hydrophobicity, Dispersion, and Electrostatics in Continuum Solvent Models
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journal
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March 2006 |
Interactions Between Neutral Phospholipid Bilayer Membranes
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journal
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March 1982 |
Anisotropic Solvent Model of the Lipid Bilayer. 2. Energetics of Insertion of Small Molecules, Peptides, and Proteins in Membranes
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journal
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March 2011 |
Flavivirus membrane fusion
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journal
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October 2006 |
Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by 2H NMR Spectroscopy
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journal
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December 2000 |
Water Ordering at Membrane Interfaces Controls Fusion Dynamics
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journal
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March 2011 |
Effect of Membrane Curvature-Modifying Lipids on Membrane Fusion by Tick-Borne Encephalitis Virus
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journal
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August 2004 |
Lipids in biological membrane fusion
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journal
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July 1995 |
Structure of the dengue virus envelope protein after membrane fusion
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journal
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January 2004 |
Hofmeister effects: interplay of hydration, nonelectrostatic potentials, and ion size
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journal
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January 2011 |
Capillary waves at the liquid-vapor interface and the surface tension of water
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journal
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July 2006 |
Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
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journal
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November 2007 |
The MARTINI Coarse-Grained Force Field: Extension to Proteins
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journal
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April 2008 |
APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
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journal
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September 2010 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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journal
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April 1998 |
In Vitro and In Vivo Studies Identify Important Features of Dengue Virus pr-E Protein Interactions
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journal
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October 2010 |
A Consistent Model for Thermal Fluctuations and Protein-Induced Deformations in Lipid Bilayers
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journal
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March 2006 |
Structures of immature flavivirus particles
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journal
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June 2003 |
Splaying of Aliphatic Tails Plays a Central Role in Barrier Crossing During Liposome Fusion
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journal
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September 2010 |
Cryo-EM Reconstruction of Dengue Virus in Complex with the Carbohydrate Recognition Domain of DC-SIGN
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journal
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February 2006 |
Role of spike protein conformational changes in fusion of Semliki Forest virus.
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journal
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January 1993 |
An Early Stage of Membrane Fusion Mediated by the Low pH Conformation of Influenza Hemagglutinin Depends upon Membrane Lipids
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journal
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January 1997 |
An overview of the Trilinos project
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journal
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September 2005 |
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
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journal
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June 2010 |
UCSF Chimera?A visualization system for exploratory research and analysis
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journal
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January 2004 |
Dengue virus infectivity depends on envelope protein binding to target cell heparan sulfate
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journal
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August 1997 |
Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions
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May 2010 |
Dendritic‐cell‐specific ICAM3‐grabbing non‐integrin is essential for the productive infection of human dendritic cells by mosquito‐cell‐derived dengue viruses
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June 2003 |
Equilibrium exchange enhances the convergence rate of umbrella sampling
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July 2008 |
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
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journal
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July 2009 |
Membrane Fusion: Stalk Model Revisited
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journal
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February 2002 |
Structure of Functional Staphylococcus aureus α-Hemolysin Channels in Tethered Bilayer Lipid Membranes
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journal
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February 2009 |
Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles
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journal
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October 1997 |
Membrane Partitioning of the Cleavage Peptide in Flock House Virus
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journal
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February 2000 |
Single-Walled Carbon Nanotube AFM Probes: Optimal Imaging Resolution of Nanoclusters and Biomolecules in Ambient and Fluid Environments
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journal
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September 2004 |
Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns
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journal
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June 2011 |
The Helical Domains of the Stem Region of Dengue Virus Envelope Protein Are Involved in both Virus Assembly and Entry
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journal
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March 2011 |
The Transmembrane Domain of Influenza Hemagglutinin Exhibits a Stringent Length Requirement to Support the Hemifusion to Fusion Transition
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journal
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October 2000 |
Synthetic Fusion Peptides of Tick-Borne Encephalitis Virus as Models for Membrane Fusion
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journal
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January 2010 |
Atomic-level functional model of dengue virus Envelope protein infectivity
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journal
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October 2013 |
Initial size and dynamics of viral fusion pores are a function of the fusion protein mediating membrane fusion
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journal
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June 2008 |
Involvement of Lipids in Different Steps of the Flavivirus Fusion Mechanism
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journal
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July 2003 |
IFITM Proteins Restrict Viral Membrane Hemifusion
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journal
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January 2013 |
Stability of trimeric DENV envelope protein at low and neutral pH: An insight from MD study
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journal
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January 2013 |
Viral membrane fusion
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journal
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July 2008 |
PH-dependent Fusion between the Flavivirus West Nile and Liposomal Model Membranes
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January 1986 |
The hemifusion intermediate and its conversion to complete fusion: regulation by membrane composition
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journal
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September 1995 |
Structure and Energy of Fusion Stalks: The Role of Membrane Edges
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journal
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December 2002 |
Variable Surface Epitopes in the Crystal Structure of Dengue Virus Type 3 Envelope Glycoprotein
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journal
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January 2005 |
Mechanics of membrane fusion
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journal
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July 2008 |
Cryo-EM structure of the mature dengue virus at 3.5-Å resolution
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journal
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December 2012 |
DC-SIGN (CD209) Mediates Dengue Virus Infection of Human Dendritic Cells
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journal
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April 2003 |
Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation
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journal
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February 2004 |
Salt screening and specific ion adsorption determine neutral-lipid membrane interactions
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journal
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May 2006 |
Differential Cholesterol Binding by Class II Fusion Proteins Determines Membrane Fusion Properties
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journal
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July 2008 |
Hydration Forces
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journal
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October 1993 |
Ion selectivity from local configurations of ligands in solutions and ion channels
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journal
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January 2010 |
Membrane Fusion Activity of Tick-Borne Encephalitis Virus and Recombinant Subviral Particles in a Liposomal Model System
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journal
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March 2000 |
Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody
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August 2009 |
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
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journal
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November 2011 |
Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains
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journal
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January 2006 |
Determining the Gaussian Curvature Modulus of Lipid Membranes in Simulations
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journal
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March 2012 |
An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers
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journal
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March 2009 |
Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
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February 2008 |
Statistically optimal analysis of samples from multiple equilibrium states
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journal
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September 2008 |
Structure of the Immature Dengue Virus at Low pH Primes Proteolytic Maturation
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journal
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March 2008 |
The Flavivirus Precursor Membrane-Envelope Protein Complex: Structure and Maturation
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journal
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March 2008 |
Productive Dengue Virus Infection of Human Endothelial Cells Is Directed by Heparan Sulfate-Containing Proteoglycan Receptors
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journal
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July 2011 |
Cholesterol is required for infection by Semliki Forest virus.
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journal
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February 1991 |
Elastic Modeling of Biomembranes and Lipid Bilayers
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journal
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May 2008 |
DOLFIN: Automated finite element computing
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journal
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April 2010 |
A quantitative model for membrane fusion based on low-energy intermediates
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June 2001 |
Dengue Virus Ensures Its Fusion in Late Endosomes Using Compartment-Specific Lipids
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October 2010 |
A smooth particle mesh Ewald method
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journal
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November 1995 |
Structure of a Dengue Virus Envelope Protein Late-Stage Fusion Intermediate
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journal
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December 2012 |
Molecular structures of fluid phase phosphatidylglycerol bilayers as determined by small angle neutron and X-ray scattering
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journal
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September 2012 |
Stalk Model of Membrane Fusion: Solution of Energy Crisis
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journal
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February 2002 |
Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach
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journal
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February 2005 |
On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations
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journal
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September 1996 |
Modeling of Peptide Adsorption Interactions with a Poly(lactic acid) Surface
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December 2008 |