The gram‐negative outer membrane modeler: Automated building of lipopolysaccharide‐rich bacterial outer membranes in four force fields

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

(2018) Jumin Lee et al.   Journal of Chemical Theory and Computation

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

(2017) Reinis Danne et al.   Journal of Chemical Information and Modeling

Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes

(2017) Denys E. S. Santos et al.   Journal of Chemical Information and Modeling

Modeling Diversity in Structures of Bacterial Outer Membrane Lipids

(2017) Huilin Ma et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

(2017) Pin-Chia Hsu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

(2017) Alister Boags et al.   Journal of Physical Chemistry Letters

Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli

(2017) Huilin Ma et al.   LANGMUIR

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

(2017) David Sehnal et al.   NATURE METHODS

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

(2016) Seonghoon Kim et al.   BIOPHYSICAL JOURNAL

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

(2016) Dhilon S. Patel et al.   BIOPHYSICAL JOURNAL

Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans

(2016) Arunima Singh et al.   CANADIAN JOURNAL OF CHEMISTRY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis

(2016) Wanatchaporn Arunmanee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

(2015) Jamie Parkin et al.   BIOPHYSICAL JOURNAL

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

(2015) Carsten Kutzner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model

(2015) Huilin Ma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid Organization of the Plasma Membrane

(2014) Helgi I. Ingólfsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Interaction of Pristine and Functionalized Carbon Nanotubes with Lipid Membranes

(2013) Svetlana Baoukina et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterizing Pilus-Mediated Adhesion of Biofilm-Forming E. coli to Chemically Diverse Surfaces Using Atomic Force Microscopy

(2013) He Xu et al.   LANGMUIR

Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

(2012) Wei Han et al.   Journal of Chemical Theory and Computation

The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View

(2012) Frederico J. S. Pontes et al.   Journal of Chemical Theory and Computation

A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation

(2012) Karl N. Kirschner et al.   Journal of Chemical Theory and Computation

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Structure of Escherichia coli OmpF porin from lipidic mesophase

(2012) Rouslan G. Efremov et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

(2012) Xavier Periole et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

(2012) Dániel Kozma et al.   NUCLEIC ACIDS RESEARCH

The Binding of Antibiotics in OmpF Porin

(2012) Brigitte K. Ziervogel et al.   STRUCTURE

Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding

(2011) Wei Huang et al.   Journal of Chemical Theory and Computation

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How β-Lactam Antibiotics Enter Bacteria: A Dialogue with the Porins

(2009) Chloë E. James et al.   PLoS One

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

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

The molecular face of lipid rafts in model membranes

(2008) H. J. Risselada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA