Coarse-Grained Models for Protein-Cell Membrane Interactions

Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling

(2013) Haosheng Cui et al.   BIOPHYSICAL JOURNAL

Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs

(2013) S.K. Sadiq et al.   CURRENT MEDICINAL CHEMISTRY

Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein

(2013) Andre A.S.T. Ribeiro et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Challenges in Multiscale Modeling of Polymer Dynamics

(2013) Ying Li et al.   Polymers

Computational Models of Protein Kinematics and Dynamics: Beyond Simulation

(2012) Bryant Gipson et al.   Annual Review of Analytical Chemistry

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Structural Basis of Membrane Bending by the N-BAR Protein Endophilin

(2012) Carsten Mim et al.   CELL

Atomistic modeling of protein–DNA interaction specificity: progress and applications

(2012) Limin Angela Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

(2012) Peter Csermely et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Multiple molecule effects on the cooperativity of protein folding transitions in simulations

(2012) Jacob I. Lewis et al.   JOURNAL OF CHEMICAL PHYSICS

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

(2012) Mikyung Seo et al.   Journal of Chemical Theory and Computation

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields

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

Hybrid Approach for Highly Coarse-Grained Lipid Bilayer Models

(2012) Anand Srivastava 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

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

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

Efficient Algorithms for Langevin and DPD Dynamics

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

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

(2012) Olga Bezkorovaynaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain

(2012) Chun-Liang Lai et al.   JOURNAL OF MOLECULAR BIOLOGY

α-Synuclein Induces Both Positive Mean Curvature and Negative Gaussian Curvature in Membranes

(2012) Anthony R. Braun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Simulation of Hydrophobin Adsorption at an Oil–Water Interface

(2012) David L. Cheung   LANGMUIR

Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields

(2012) Jin Liu et al.   MOLECULAR PHYSICS

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes

(2012) Michael Leguèbe et al.   PLoS One

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Structural modelling and dynamics of proteins for insights into drug interactions

(2011) Tim Werner et al.   ADVANCED DRUG DELIVERY REVIEWS

Thermodynamics and Mechanics of Membrane Curvature Generation and Sensing by Proteins and Lipids

(2011) Tobias Baumgart et al.   Annual Review of Physical Chemistry

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations

(2011) Erik G. Brandt et al.   BIOPHYSICAL JOURNAL

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Free energy calculations of protein–ligand interactions

(2011) Anita de Ruiter et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using the Wimley–White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model

(2011) Gurpreet Singh et al.   Journal of Chemical Theory and Computation

Exploration of Transferability in Multiscale Coarse-Grained Peptide Models

(2011) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer

(2011) Jason D. Perlmutter et al.   LANGMUIR

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

(2011) Andrzej J. Rzepiela et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding

(2011) Ivan Coluzza   PLoS One

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making connections between ultrafast protein folding kinetics and molecular dynamics simulations

(2011) T. Cellmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Raft registration across bilayers in a molecularly detailed model

(2011) Diego A. Pantano et al.   Soft Matter

The atomistic simulation of DNA

(2011) Charles A. Laughton et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Protein Mechanics: From Single Molecules to Functional Biomaterials

(2010) Hongbin Li et al.   ACCOUNTS OF CHEMICAL RESEARCH

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Folding of lipid monolayers containing lung surfactant proteins SP-B 1 – 25 and SP-C studied via coarse-grained molecular dynamics simulations

(2010) Susan L. Duncan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Partitioning of Lipids at Domain Boundaries in Model Membranes

(2010) Lars V. Schäfer et al.   BIOPHYSICAL JOURNAL

Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides

(2010) Sivaramakrishnan Ramadurai et al.   BIOPHYSICAL JOURNAL

Direct Simulation of Protein-Mediated Vesicle Fusion: Lung Surfactant Protein B

(2010) Svetlana Baoukina et al.   BIOPHYSICAL JOURNAL

Multiscale Computer Simulation of the Immature HIV-1 Virion

(2010) Gary S. Ayton et al.   BIOPHYSICAL JOURNAL

Molecular Simulation of the Effect of Cholesterol on Lipid-Mediated Protein-Protein Interactions

(2010) Frédérick J.-M. de Meyer et al.   BIOPHYSICAL JOURNAL

Protein dynamics: dancing on an ever-changing free energy stage

(2010) Dennis R Livesay   CURRENT OPINION IN PHARMACOLOGY

Reaching biological timescales with all-atom molecular dynamics simulations

(2010) Matthew C Zwier et al.   CURRENT OPINION IN PHARMACOLOGY

Using NMR to study fast dynamics in proteins: methods and applications

(2010) Paul J Sapienza et al.   CURRENT OPINION IN PHARMACOLOGY

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

Large conformational changes in proteins: signaling and other functions

(2010) Barry J Grant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Immobilization of the Plug Domain Inside the SecY Channel Allows Unrestricted Protein Translocation

(2010) Jelger A. Lycklama a Nijeholt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The multiscale coarse-graining method: Assessing its accuracy and introducing density dependent coarse-grain potentials

(2010) Sergei Izvekov et al.   JOURNAL OF CHEMICAL PHYSICS

An implicit solvent coarse-grained lipid model with correct stress profile

(2010) Alex J. Sodt et al.   JOURNAL OF CHEMICAL PHYSICS

Reconstruction of atomistic details from coarse-grained structures

(2010) Andrzej J. Rzepiela et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Determining Peptide Partitioning Properties via Computer Simulation

(2010) Jakob P. Ulmschneider et al.   JOURNAL OF MEMBRANE BIOLOGY

Atomistic Simulation of Hydrophobic Matching Effects on Lipid Composition near a Helical Peptide Embedded in Mixed-Lipid Bilayers

(2010) Fuchang Yin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations

(2010) Adil Khalfa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

(2010) Wataru Shinoda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane

(2010) Anton A. Polyansky et al.   Journal of Physical Chemistry Letters

Solvent-Exposed Tails as Prestalk Transition States for Membrane Fusion at Low Hydration

(2010) Yuliya G. Smirnova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides

(2010) Martin B. Ulmschneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA Lipoplexes: Formation of the Inverse Hexagonal Phase Observed by Coarse-Grained Molecular Dynamics Simulation

(2010) Josephine Corsi et al.   LANGMUIR

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

(2010) Durba Sengupta et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Release of content through mechano-sensitive gates in pressurized liposomes

(2010) M. Louhivuori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain

(2010) HyeongJun Kim et al.   STRUCTURE

Role of Lipids in Spheroidal High Density Lipoproteins

(2010) Timo Vuorela et al.   PLoS Computational Biology

Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis

(2010) Neeraj J. Agrawal et al.   PLoS Computational Biology

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

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

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

(2010) Del Lucent et al.   PLoS Computational Biology

Molecular simulation of adsorption and its implications to protein chromatography: A review

(2009) Lin Zhang et al.   BIOCHEMICAL ENGINEERING JOURNAL

Experimental verification of lipid bilayer structure through multi-scale modeling

(2009) Jason D. Perlmutter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Membrane-Bending Mechanism of Amphiphysin N-BAR Domains

(2009) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models

(2009) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics

(2009) Georgi Z. Genchev et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

(2009) Gary S. Ayton et al.   FARADAY DISCUSSIONS

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales

(2009) Gary S. Ayton et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Single Bicontinuous Cubic Phase Induced by Fusion Peptides

(2009) Marc Fuhrmans et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation

(2009) Alessandra Villa et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Calculation of free energies in fluid membranes subject to heterogeneous curvature fields

(2009) Neeraj J. Agrawal et al.   PHYSICAL REVIEW E

3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes

(2009) O. H. Samuli Ollila et al.   PHYSICAL REVIEW LETTERS

Coarse-grained modeling of allosteric regulation in protein receptors

(2009) I. A. Balabin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains

(2009) Ying Yin et al.   STRUCTURE

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Helix−Helix Interactions in Membrane Proteins: Coarse-Grained Simulations of Glycophorin A Helix Dimerization†

(2008) Emi Psachoulia et al.   BIOCHEMISTRY

Coarse-Grained Molecular Dynamics Simulations of the Energetics of Helix Insertion into a Lipid Bilayer†

(2008) Peter J. Bond et al.   BIOCHEMISTRY

Mechanosensitive Membrane Channels in Action

(2008) Serge Yefimov et al.   BIOPHYSICAL JOURNAL

The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations

(2008) Chze Ling Wee et al.   BIOPHYSICAL JOURNAL

Four-Scale Description of Membrane Sculpting by BAR Domains

(2008) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

(2008) Edward Lyman et al.   BIOPHYSICAL JOURNAL

Liquid-Liquid Domains in Bilayers Detected by Wide Angle X-Ray Scattering

(2008) Thalia T. Mills et al.   BIOPHYSICAL JOURNAL

Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations

(2008) Justin L. MacCallum et al.   BIOPHYSICAL JOURNAL

Molecular Simulations of Lipid-Mediated Protein-Protein Interactions

(2008) Frédérick Jean-Marie de Meyer et al.   BIOPHYSICAL JOURNAL

Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study

(2008) Lea Thøgersen et al.   BIOPHYSICAL JOURNAL

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data

(2008) Norbert Kučerka et al.   BIOPHYSICAL JOURNAL

Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

(2008) Beate West et al.   BIOPHYSICAL JOURNAL

Mechanosensitive Channels: Insights from Continuum-Based Simulations

(2008) Yuye Tang et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Association energetics of membrane spanning α-helices

(2008) K MACKENZIE et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Membrane proteins: molecular dynamics simulations

(2008) E LINDAHL et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains

(2008) Wei Han et al.   Journal of Chemical Theory and Computation

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Coarse-Grained Molecular Dynamics Studies of the Concentration and Size Dependence of Fifth- and Seventh-Generation PAMAM Dendrimers on Pore Formation in DMPC Bilayer

(2008) Hwankyu Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Gating Motions in Voltage-Gated Potassium Channels Revealed by Coarse-Grained Molecular Dynamics Simulations

(2008) Werner Treptow et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid Bilayer Curvature and Pore Formation Induced by Charged Linear Polymers and Dendrimers: The Effect of Molecular Shape

(2008) Hwankyu Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing Peptide Nanotube Self-Assembly at a Liquid−Liquid Interface with Coarse-Grained Molecular Dynamics

(2008) Ekta Khurana et al.   NANO LETTERS

Blocking of Carbon Nanotube Based Nanoinjectors by Lipids: A Simulation Study

(2008) E. Jayne Wallace et al.   NANO LETTERS

Computer simulation study of fullerene translocation through lipid membranes

(2008) Jirasak Wong-Ekkabut et al.   Nature Nanotechnology

The molecular mechanism of lipid monolayer collapse

(2008) S. Baoukina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

A Quantitative Coarse-Grain Model for Lipid Bilayers

(2007) Mario Orsi et al.   JOURNAL OF PHYSICAL CHEMISTRY B