Published in Chem Soc Rev on August 21, 2013
Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure (2015) 1.54
Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem Biol (2014) 1.39
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure (2015) 1.08
Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Sci Rep (2013) 1.05
Molecular dynamics simulations of large macromolecular complexes. Curr Opin Struct Biol (2015) 0.99
Microsecond molecular dynamics simulations of lipid mixing. Langmuir (2014) 0.97
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev (2014) 0.88
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. J Membr Biol (2015) 0.87
Foundations of biomolecular modeling. Cell (2013) 0.85
Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development. MAbs (2016) 0.84
Lipases immobilization for effective synthesis of biodiesel starting from coffee waste oils. Biomolecules (2013) 0.82
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries. J Chem Theory Comput (2015) 0.82
NRas slows the rate at which a model lipid bilayer phase separates. Faraday Discuss (2014) 0.81
Hydrophobic compounds reshape membrane domains. PLoS Comput Biol (2014) 0.81
Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model. J Chem Theory Comput (2015) 0.81
Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer. Biophys Chem (2015) 0.81
Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations. Biochim Biophys Acta (2016) 0.81
Atomic-level description of protein-lipid interactions using an accelerated membrane model. Biochim Biophys Acta (2016) 0.81
Continuum approaches to understanding ion and peptide interactions with the membrane. J Membr Biol (2014) 0.80
Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. J Membr Biol (2015) 0.80
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discuss (2014) 0.80
LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol (2014) 0.80
The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope. Structure (2016) 0.80
Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front Physiol (2016) 0.79
Refining the treatment of membrane proteins by coarse-grained models. Proteins (2015) 0.79
Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations. J Am Chem Soc (2016) 0.79
Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor. J Phys Chem B (2016) 0.78
Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics. Structure (2016) 0.78
Biological Responses to Engineered Nanomaterials: Needs for the Next Decade. ACS Cent Sci (2015) 0.78
MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins. J Appl Crystallogr (2014) 0.78
Chloroform alters interleaflet coupling in lipid bilayers: an entropic mechanism. J R Soc Interface (2015) 0.78
Oligomerization of the Tetraspanin CD81 via the Flexibility of Its δ-Loop. Biophys J (2016) 0.78
Coarse-grained molecular dynamics studies of the translocation mechanism of polyarginines across asymmetric membrane under tension. Sci Rep (2015) 0.78
The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane. Phys Chem Chem Phys (2016) 0.77
Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics. Langmuir (2015) 0.77
More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. J Chem Phys (2014) 0.77
Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning. J Phys Chem B (2016) 0.77
Organization of lipids in the tear film: a molecular-level view. PLoS One (2014) 0.77
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association. J Phys Chem B (2016) 0.77
Seeing the Forest in Lieu of the Trees: Continuum Simulations of Cell Membranes at Large Length Scales. Annu Rep Comput Chem (2014) 0.77
Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations. J Chem Theory Comput (2014) 0.77
The (Mathematical) Modeling Process in Biosciences. Front Genet (2015) 0.77
Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness. Proc Natl Acad Sci U S A (2015) 0.77
Interactions of borneol with DPPC phospholipid membranes: a molecular dynamics simulation study. Int J Mol Sci (2014) 0.77
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochim Biophys Acta (2016) 0.77
The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation. Int J Mol Sci (2014) 0.76
Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits. J Chem Phys (2015) 0.76
Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors. Structure (2015) 0.76
Mathematical and computational modeling in biology at multiple scales. Theor Biol Med Model (2014) 0.76
Structures of the EphA2 Receptor at the Membrane: Role of Lipid Interactions. Structure (2015) 0.76
Computational virology: From the inside out. Biochim Biophys Acta (2016) 0.76
Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus (2016) 0.76
Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. J Comput Aided Mol Des (2014) 0.76
Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes. Biochemistry (2016) 0.76
Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane. J Phys Chem B (2016) 0.76
Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Curr Opin Struct Biol (2016) 0.76
Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles. J Chem Theory Comput (2016) 0.76
Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity. Sci Adv (2017) 0.75
Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. J Am Chem Soc (2017) 0.75
Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes. Sci Rep (2016) 0.75
The cellular membrane as a mediator for small molecule interaction with membrane proteins. Biochim Biophys Acta (2016) 0.75
Stability and dynamics of membrane-spanning DNA nanopores. Nat Commun (2017) 0.75
Coarse-grained simulations of hemolytic peptide δ-lysin interacting with a POPC bilayer. Biochim Biophys Acta (2016) 0.75
High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. J Am Chem Soc (2017) 0.75
Lipid Raft Size and Lipid Mobility in Non-raft Domains Increase during Aging and Are Exacerbated in APP/PS1 Mice Model of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model. Front Physiol (2016) 0.75
The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study. PLoS One (2016) 0.75
Recent advances in transferable coarse-grained modeling of proteins. Adv Protein Chem Struct Biol (2014) 0.75
The C-terminal Domains of Apoptotic BH3-only Proteins Mediate Their Insertion into Distinct Biological Membranes. J Biol Chem (2016) 0.75
The Molecular Mechanism Underlying Recruitment and Insertion of Lipid-Anchored LC3 Protein into Membranes. Biophys J (2015) 0.75
Metal Ion Modeling Using Classical Mechanics. Chem Rev (2017) 0.75
The aliphatic chain of cholesterol modulates bilayer interleaflet coupling and domain registration. FEBS Lett (2016) 0.75
In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation. Acta Crystallogr D Biol Crystallogr (2015) 0.75
A new mixed all-atom/coarse-grained model: application to melittin aggregation in aqueous solution. J Chem Theory Comput (2017) 0.75
Martini Coarse-Grained Force Field: Extension to RNA. Biophys J (2017) 0.75
The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B (2007) 9.56
Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J (2008) 2.53
Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol (2007) 2.25
Setting up and running molecular dynamics simulations of membrane proteins. Methods (2007) 2.02
Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta (2008) 1.76
Computer simulations of membrane proteins. Biochim Biophys Acta (2004) 1.71
Computer simulation study of fullerene translocation through lipid membranes. Nat Nanotechnol (2008) 1.58
Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. Biophys J (2004) 1.55
An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins. J Biol Chem (2007) 1.50
The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter. FASEB J (2009) 1.43
K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study. Biophys J (2002) 1.42
Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J (2002) 1.37
Self-association of transmembrane alpha-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch. J Biol Chem (2005) 1.36
Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study. Biophys J (2007) 1.35
Nanopore-facilitated, voltage-driven phosphatidylserine translocation in lipid bilayers--in cells and in silico. Phys Biol (2006) 1.34
Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. J Am Chem Soc (2009) 1.33
Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles. J Am Chem Soc (2006) 1.30
Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J Phys Condens Matter (2006) 1.28
Structural arrangement of the transmission interface in the antigen ABC transport complex TAP. Proc Natl Acad Sci U S A (2009) 1.27
The molecular mechanism of lipid monolayer collapse. Proc Natl Acad Sci U S A (2008) 1.26
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues. J Comput Chem (2007) 1.24
Nanopore formation and phosphatidylserine externalization in a phospholipid bilayer at high transmembrane potential. J Am Chem Soc (2006) 1.22
2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in POPC bilayers. Biophys J (2004) 1.21
Lipid organization of the plasma membrane. J Am Chem Soc (2014) 1.20
Molecular dynamics simulations of pentapeptides at interfaces: salt bridge and cation-pi interactions. Biochemistry (2003) 1.20
Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition. Biophys J (2002) 1.17
Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field. J Comput Chem (2003) 1.16
Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations. Biochem J (2003) 1.15
Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC Biochem (2005) 1.13
Conical lipids in flat bilayers induce packing defects similar to that induced by positive curvature. Biophys J (2013) 1.10
A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein. Biophys J (2005) 1.09
Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations. Biochim Biophys Acta (2009) 1.09
A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. Eur Biophys J (2003) 1.08
Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor. FEBS Lett (2004) 1.08
Structures of neat and hydrated 1-octanol from computer simulations. J Am Chem Soc (2002) 1.08
Distribution of pentachlorophenol in phospholipid bilayers: a molecular dynamics study. Biophys J (2004) 1.07
Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 1.07
Docking of mu-conotoxin GIIIA in the sodium channel outer vestibule. Channels (Austin) (2007) 1.07
Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions. Trends Biochem Sci (2011) 1.07
Transfer of arginine into lipid bilayers is nonadditive. Biophys J (2011) 1.05
Hydrophobic association of alpha-helices, steric dewetting, and enthalpic barriers to protein folding. Proc Natl Acad Sci U S A (2007) 1.05
The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter. J Biol Chem (2006) 1.04
Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Lett (2002) 1.03
Computer simulations of lipid membrane domains. Biochim Biophys Acta (2013) 1.03
ATP-binding cassette transporters in Escherichia coli. Biochim Biophys Acta (2008) 1.02
P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK. FEBS Lett (2007) 1.02
The TatA subunit of Escherichia coli twin-arginine translocase has an N-in topology. Biochemistry (2007) 1.02
Electroporating fields target oxidatively damaged areas in the cell membrane. PLoS One (2009) 1.01
Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir (2007) 1.00
Conformational transitions induced by the binding of MgATP to the vitamin B12 ATP-binding cassette (ABC) transporter BtuCD. J Biol Chem (2004) 1.00
Molecular dynamics simulations of the Apo-, Holo-, and acyl-forms of Escherichia coli acyl carrier protein. J Biol Chem (2008) 0.97
Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers. Chem Phys Lipids (2013) 0.97
The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations. Biophys J (2007) 0.97
Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD. Biophys J (2007) 0.97
Microsecond molecular dynamics simulations of lipid mixing. Langmuir (2014) 0.97
Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes. J Am Chem Soc (2009) 0.96
Computer simulation of antimicrobial peptides. Curr Med Chem (2007) 0.96
Interpretation of 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations. Biophys J (2010) 0.95
Direct simulation of transmembrane helix association: role of asparagines. Biophys J (2004) 0.93
Lipid Nanoparticles Containing siRNA Synthesized by Microfluidic Mixing Exhibit an Electron-Dense Nanostructured Core. J Phys Chem C Nanomater Interfaces (2012) 0.93
Molecular view of phase coexistence in lipid monolayers. J Am Chem Soc (2012) 0.92
Molecular basis of voltage gating of OmpF porin. Biochem Cell Biol (2002) 0.91
Direct simulation of protein-mediated vesicle fusion: lung surfactant protein B. Biophys J (2010) 0.89
Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF. Biochemistry (2006) 0.89
The human transporter associated with antigen processing: molecular models to describe peptide binding competent states. J Biol Chem (2012) 0.89
Implicit solvent model estimates of the stability of model structures of the alamethicin channel. Eur Biophys J (2003) 0.89
Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes. J Lipid Res (2012) 0.88
Combination of the CHARMM27 force field with united-atom lipid force fields. J Comput Chem (2010) 0.88
The role of extra-membranous inter-helical loops in helix-helix interactions. Protein Eng Des Sel (2005) 0.87
Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models" by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Phys Chem Chem Phys (2010) 0.87
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides. J Chem Theory Comput (2012) 0.86
Computer simulations of the phase separation in model membranes. Faraday Discuss (2013) 0.84
Residue G346 in transmembrane segment six is involved in inter-domain communication in P-glycoprotein. Biochemistry (2007) 0.84
Lateral pressure profiles in lipid monolayers. Faraday Discuss (2010) 0.84
Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations. J Phys Chem B (2005) 0.83
Oleic acid phase behavior from molecular dynamics simulations. Langmuir (2014) 0.83
Holo-BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD. Proteins (2010) 0.82
Lung surfactant protein SP-B promotes formation of bilayer reservoirs from monolayer and lipid transfer between the interface and subphase. Biophys J (2011) 0.82
The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations. Soft Matter (2014) 0.82
Molecular structure of membrane tethers. Biophys J (2012) 0.82
Structural basis for autoinhibition of CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in phosphatidylcholine synthesis, by its membrane-binding amphipathic helix. J Biol Chem (2013) 0.81
Conformational choreography of a molecular switch region in myelin basic protein--molecular dynamics shows induced folding and secondary structure type conversion upon threonyl phosphorylation in both aqueous and membrane-associated environments. Biochim Biophys Acta (2010) 0.81
Computer modeling of polyleucine-based coiled coil dimers in a realistic membrane environment: insight into helix-helix interactions in membrane proteins. Biochemistry (2004) 0.81
Water in ion channels and pores--simulation studies. Novartis Found Symp (2002) 0.80
Molecular simulations of lipid flip-flop in the presence of model transmembrane helices. Biochemistry (2010) 0.80
Molecular dynamics simulations of beta-ketoacyl-, beta-hydroxyacyl-, and trans-2-enoyl-acyl carrier proteins of Escherichia coli. Biochemistry (2010) 0.80
The distribution and conformation of very long-chain plant wax components in a lipid bilayer. J Phys Chem B (2007) 0.79
Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors. J Am Chem Soc (2005) 0.79
The importance of membrane defects-lessons from simulations. Acc Chem Res (2014) 0.79
Force fields for classical molecular dynamics. Methods Mol Biol (2013) 0.79
Transmembrane helix 12 modulates progression of the ATP catalytic cycle in ABCB1. Biochemistry (2009) 0.78
Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore. Nanoscale (2014) 0.78
Computer simulations of ABC transporter components. Biochem Cell Biol (2006) 0.78
Cytosolic region of TM6 in P-glycoprotein: topographical analysis and functional perturbation by site directed labeling. Biochemistry (2008) 0.78
Interaction of pristine and functionalized carbon nanotubes with lipid membranes. J Phys Chem B (2013) 0.77
Molecular dynamics simulations of bovine lactoferricin: turning a helix into a sheet. Biometals (2004) 0.77
Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions. Phys Chem Chem Phys (2009) 0.77
Characterization of the immersion properties of the peripheral membrane anchor of the FATC domain of the kinase "target of rapamycin" by NMR, oriented CD spectroscopy, and MD simulations. J Phys Chem B (2014) 0.75
Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins. Eur Biophys J (2009) 0.75
Density based visualization for molecular simulation. Faraday Discuss (2014) 0.75