Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study

How reliable are molecular dynamics simulations of membrane active antimicrobial peptides?

(2014) Yukun Wang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

(2014) Heidi Koldsø et al.   PLoS Computational Biology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Electrostatics and flexibility drive membrane recognition and early penetration by the antimicrobial peptide dendrimer bH1

(2013) Harish K. Ravi et al.   CHEMICAL COMMUNICATIONS

Pharmacology of polymyxins: new insights into an ‘old’ class of antibiotics

(2013) Tony Velkov et al.   Future Microbiology

Characterization of Polymyxin B-Induced Nephrotoxicity: Implications for Dosing Regimen Design

(2012) Kamilia Abdelraouf et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment

(2012) Daniel A. Holdbrook et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study

(2012) Thomas J. Piggot et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Biophysical characterization of polymyxin b interaction with LPS aggregates and membrane model systems

(2012) Marco M. Domingues et al.   BIOPOLYMERS

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

(2012) Thomas J. Piggot et al.   Journal of Chemical Theory and Computation

Antimicrobial and Cell-Penetrating Peptides: Structure, Assembly and Mechanisms of Membrane Lysis via Atomistic and Coarse-Grained Molecular Dynamic Simulations

(2012) Peter J. Bond et al.   PROTEIN AND PEPTIDE LETTERS

Multiscale molecular dynamics simulations of micelles: coarse-grain for self-assembly and atomic resolution for finer details

(2012) Pilar Brocos et al.   Soft Matter

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics

(2011) Joshua N. Horn et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers

(2011) Chris Neale et al.   Journal of Chemical Theory and Computation

Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes

(2011) Thomas J. Piggot et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Novel Anti-bacterial Activities of β-defensin 1 in Human Platelets: Suppression of Pathogen Growth and Signaling of Neutrophil Extracellular Trap Formation

(2011) Bjoern F. Kraemer et al.   PLoS Pathogens

Mechanical Properties of Coarse-Grained Bilayers Formed by Cardiolipin and Zwitterionic Lipids

(2010) Martin Dahlberg et al.   Journal of Chemical Theory and Computation

Contribution of Each Amino Acid Residue in Polymyxin B3 to Antimicrobial and Lipopolysaccharide Binding Activity

(2009) Kazushi Kanazawa et al.   CHEMICAL & PHARMACEUTICAL BULLETIN

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

(2009) Andrzej J. Rzepiela et al.   FARADAY DISCUSSIONS

Interactions of Lipopolysaccharide and Polymyxin Studied by NMR Spectroscopy

(2009) Jiri Mares et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins

(2009) Andreas Kukol   Journal of Chemical Theory and Computation

Structure−Activity Relationships of Polymyxin Antibiotics

(2009) Tony Velkov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Coarse-Grained Simulations of the Membrane-Active Antimicrobial Peptide Maculatin 1.1

(2008) Peter J. Bond et al.   BIOPHYSICAL JOURNAL

Polymyxins Revisited

(2008) D. Landman et al.   CLINICAL MICROBIOLOGY REVIEWS

Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes

(2008) T.A. Soares et al.   MOLECULAR SIMULATION

Computer Simulation of Uranyl Uptake by the Rough Lipopolysaccharide Membrane ofPseudomonas aeruginosa

(2007) Roberto D. Lins et al.   BIOMACROMOLECULES

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation