Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration

Molecular architecture of the human caveolin-1 complex

(2022) Jason C. Porta et al.   Science Advances

freud: A software suite for high throughput analysis of particle simulation data

(2020) Vyas Ramasubramani et al.   COMPUTER PHYSICS COMMUNICATIONS

Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint

(2020) Mayank Dixit et al.   JOURNAL OF CHEMICAL PHYSICS

Improving immunogenicity of influenza virus H7N9 recombinant hemagglutinin for vaccine development

(2019) Ting-Hui-Lin et al.   VACCINE

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

Cell Fusion: Merging Membranes and Making Muscle

(2019) Michael J. Petrany et al.   TRENDS IN CELL BIOLOGY

Permeability of membranes in the liquid ordered and liquid disordered phases

(2019) An Ghysels et al.   Nature Communications

Membrane Elastic Deformations Modulate Gramicidin A Transbilayer Dimerization And Lateral Clustering

(2018) Oleg V. Kondrashov et al.   BIOPHYSICAL JOURNAL

Lipid-dependence of target membrane stability during influenza viral fusion

(2018) Sourav Haldar et al.   JOURNAL OF CELL SCIENCE

Metastable Prepores in Tension-Free Lipid Bilayers

(2018) Christina L. Ting et al.   PHYSICAL REVIEW LETTERS

Myomaker and Myomerger Work Independently to Control Distinct Steps of Membrane Remodeling during Myoblast Fusion

(2018) Evgenia Leikina et al.   DEVELOPMENTAL CELL

Depth-Dependent Membrane Ordering by Hemagglutinin Fusion Peptide Promotes Fusion

(2017) Hirak Chakraborty et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Measuring the potential energy barrier to lipid bilayer electroporation

(2017) Jason T. Sengel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Pore formation in lipid membrane I: Continuous reversible trajectory from intact bilayer through hydrophobic defect to transversal pore

(2017) Sergey A. Akimov et al.   Scientific Reports

Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores

(2016) B. Scott Perrin et al.   BIOPHYSICAL JOURNAL

The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes

(2016) Petr Chlanda et al.   Nature Microbiology

Mechanical properties of lipid bilayers from molecular dynamics simulation

(2015) Richard M. Venable et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Viral membrane fusion

(2015) Stephen C. Harrison   VIROLOGY

MEMBPLUGIN: studying membrane complexity in VMD

(2014) Ramon Guixà-González et al.   BIOINFORMATICS

Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

(2014) W. F. Drew Bennett et al.   BIOPHYSICAL JOURNAL

Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

(2014) Tod D. Romo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR

(2014) Allyn R. Brice et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistical Analysis of Peptide-Induced Graded and All-or-None Fluxes in Giant Vesicles

(2013) Sterling A. Wheaten et al.   BIOPHYSICAL JOURNAL

Fusion Peptides Promote Formation of Bilayer Cubic Phases in Lipid Dispersions. An X-Ray Diffraction Study

(2013) Boris G. Tenchov et al.   BIOPHYSICAL JOURNAL

Gel-Assisted Formation of Giant Unilamellar Vesicles

(2013) Andreas Weinberger et al.   BIOPHYSICAL JOURNAL

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

(2013) Ross A. Lippert et al.   JOURNAL OF CHEMICAL PHYSICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Accurate Determination of the Orientational Distribution of a Fluorescent Molecule in a Phospholipid Membrane

(2013) Štěpán Timr et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Geometric Catalysis of Membrane Fission Driven by Flexible Dynamin Rings

(2013) A. V. Shnyrova et al.   SCIENCE

Monolayer spontaneous curvature of raft-forming membrane lipids

(2013) Benjamin Kollmitzer et al.   Soft Matter

Probing the Orientational Distribution of Dyes in Membranes through Multiphoton Microscopy

(2012) James E. Reeve et al.   BIOPHYSICAL JOURNAL

Distribution of surface glycoproteins on influenza A virus determined by electron cryotomography

(2012) Sebastian Wasilewski et al.   VACCINE

Update of the Cholesterol Force Field Parameters in CHARMM

(2011) Joseph B. Lim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

All-or-None versus Graded: Single-Vesicle Analysis Reveals Lipid Composition Effects on Membrane Permeabilization

(2010) Beatriz Apellániz et al.   BIOPHYSICAL JOURNAL

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface

(2010) J. L. Lorieau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composition and Functions of the Influenza Fusion Peptide

(2010) Karen Cross et al.   PROTEIN AND PEPTIDE LETTERS

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse-Grained Simulation Studies of Peptide-Induced Pore Formation

(2008) Gregoria Illya et al.   BIOPHYSICAL JOURNAL

GTPase Cycle of Dynamin Is Coupled to Membrane Squeeze and Release, Leading to Spontaneous Fission

(2008) Pavel V. Bashkirov et al.   CELL

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY