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β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure (2012) 1.04

Modeling and simulation of ion channels. Chem Rev (2012) 1.02

Hydrophobic gating in ion channels. J Mol Biol (2014) 1.00

Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc Natl Acad Sci U S A (2013) 0.91

Theory and simulation of ion conduction in the pentameric GLIC channel. J Chem Theory Comput (2012) 0.91

Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future. Int J Mol Sci (2016) 0.88

Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation. Front Pharmacol (2012) 0.87

In silico cross seeding of Aβ and amylin fibril-like oligomers. ACS Chem Neurosci (2013) 0.86

Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase. PLoS Comput Biol (2012) 0.85

The stability of cylindrin β-barrel amyloid oligomer models-a molecular dynamics study. Proteins (2013) 0.84

Mutations and seeding of amylin fibril-like oligomers. J Phys Chem B (2013) 0.83

Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J (2011) 0.80

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. J Gen Physiol (2013) 0.80

Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition. J Struct Biol (2013) 0.80

Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC). Biochim Biophys Acta (2016) 0.79

Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method. J Chem Theory Comput (2015) 0.79

Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane. J Biol Chem (2016) 0.78

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes. Biophys J (2015) 0.78

Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure (2016) 0.78

Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations. PLoS Comput Biol (2014) 0.78

Stability of Iowa mutant and wild type Aβ-peptide aggregates. J Chem Phys (2014) 0.78

Collective diffusion model for ion conduction through microscopic channels. Biophys J (2013) 0.77

Inter-species cross-seeding: stability and assembly of rat-human amylin aggregates. PLoS One (2014) 0.77

Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels. Biophys J (2016) 0.77

Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level. PLoS Comput Biol (2015) 0.77

Pentameric Ligand-gated Ion Channels : Insights from Computation. Mol Simul (2014) 0.76

On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains. Protein Sci (2015) 0.76

Effect of single point mutations in a form of systemic amyloidosis. Protein Sci (2015) 0.75

Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1. Biophys J (2016) 0.75

Exploring the structure of the voltage-gated Na+ channel by an engineered drug access pathway to the receptor site for local anesthetics. J Biol Chem (2014) 0.75

Membrainy: a 'smart', unified membrane analysis tool. Source Code Biol Med (2015) 0.75

Functional Annotation of Ion Channel Structures by Molecular Simulation. Structure (2016) 0.75

Gating Charge Calculations by Computational Electrophysiology Simulations. Biophys J (2017) 0.75

Molecular dynamics simulations of early steps in RNA-mediated conversion of prions. Protein Sci (2017) 0.75

Energetics and mechanism of anion permeation across formate-nitrite transporters. Sci Rep (2017) 0.75

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput (2008) 34.90

Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80

Canonical sampling through velocity rescaling. J Chem Phys (2007) 12.40

Crystal structures explain functional properties of two E. coli porins. Nature (1992) 10.38

Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J (1997) 9.60

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation. J Chem Theory Comput (2008) 4.56

Voltage-gated potassium channels as therapeutic targets. Nat Rev Drug Discov (2009) 3.12

The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria. Nat Rev Microbiol (2008) 2.82

Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J Mol Biol (2002) 2.61

Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci U S A (2010) 2.47

Osmotic water transport through carbon nanotube membranes. Proc Natl Acad Sci U S A (2003) 2.41

Theoretical and computational models of biological ion channels. Q Rev Biophys (2004) 2.41

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem (2010) 2.08

Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. J Am Chem Soc (2003) 2.00

A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys J (2000) 1.92

The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol (2003) 1.80

The membrane potential and its representation by a constant electric field in computer simulations. Biophys J (2008) 1.68

Porin-mediated antibiotic resistance in Neisseria gonorrhoeae: ion, solute, and antibiotic permeation through PIB proteins with penB mutations. J Bacteriol (2006) 1.61

Ion channels as drug targets: the next GPCRs. J Gen Physiol (2008) 1.51

Atomistic simulations of biologically realistic transmembrane potential gradients. J Chem Phys (2004) 1.43

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43

Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol (2009) 1.41

The role of porins in neisserial pathogenesis and immunity. Trends Microbiol (2003) 1.30

Electric field-controlled water permeation coupled to ion transport through a nanopore. J Chem Phys (2004) 1.16

Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB. Proc Natl Acad Sci U S A (2010) 1.14

Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis. PLoS Pathog (2009) 1.09

Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophys J (2002) 1.08

Short openings in high resolution single channel recordings of mouse nicotinic receptors. J Physiol (2005) 1.01

Successful recovery of the normal electrophysiological properties of PorB (class 3) porin from Neisseria meningitidis after expression in Escherichia coli and renaturation. Biochim Biophys Acta (1998) 0.95

Improved 3D continuum calculations of ion flux through membrane channels. Eur Biophys J (2003) 0.94

Replica exchange with nonequilibrium switches. Proc Natl Acad Sci U S A (2009) 0.92

High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32. J Biol Chem (2006) 0.90

Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: methodological issues. J Chem Phys (2009) 0.87

Multistep mechanism of chloride translocation in a strongly anion-selective porin channel. Biophys J (2003) 0.84

Molecular anatomy of a trafficking organelle. Cell (2006) 11.47

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04

Anatomy and dynamics of a supramolecular membrane protein cluster. Science (2007) 3.75

Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des (2010) 2.67

Membrane protein sequestering by ionic protein-lipid interactions. Nature (2011) 2.40

Effect of sodium chloride on a lipid bilayer. Biophys J (2003) 2.24

Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21

Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J (2006) 2.19

Mechanoenzymatics of titin kinase. Proc Natl Acad Sci U S A (2008) 2.17

Generalized correlation for biomolecular dynamics. Proteins (2006) 2.17

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem (2010) 2.08

Predicting free energy changes using structural ensembles. Nat Methods (2009) 1.93

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nat Struct Biol (2002) 1.92

The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol (2003) 1.80

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75

Force spectroscopy of single biomolecules. Chemphyschem (2002) 1.73

Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys J (2004) 1.70

Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A (2008) 1.67

The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr Opin Struct Biol (2005) 1.65

Single-molecule FRET measures bends and kinks in DNA. Proc Natl Acad Sci U S A (2008) 1.58

Structure and function of water channels. Curr Opin Struct Biol (2002) 1.55

Multistep binding of divalent cations to phospholipid bilayers: a molecular dynamics study. Angew Chem Int Ed Engl (2004) 1.50

A designed inhibitor of a CLC antiporter blocks function through a unique binding mode. Chem Biol (2012) 1.49

Full correlation analysis of conformational protein dynamics. Proteins (2008) 1.47

Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem (2006) 1.46

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43

Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol (2013) 1.41

Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol (2009) 1.41

Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nat Struct Mol Biol (2011) 1.41

Interaction of urea with amino acids: implications for urea-induced protein denaturation. J Am Chem Soc (2007) 1.39

Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat Struct Mol Biol (2013) 1.38

Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J (2002) 1.37

Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33

Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33

Membrane fusion. Curr Opin Cell Biol (2002) 1.29

Does CO2 permeate through aquaporin-1? Biophys J (2006) 1.28

Detection of functional modes in protein dynamics. PLoS Comput Biol (2009) 1.27

How SNARE molecules mediate membrane fusion: recent insights from molecular simulations. Curr Opin Struct Biol (2012) 1.26

Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J (2009) 1.26

Geometry-based sampling of conformational transitions in proteins. Structure (2007) 1.26

Caught in the act: visualization of SNARE-mediated fusion events in molecular detail. Chembiochem (2011) 1.25

Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23

Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA (2005) 1.23

Simulation of fluorescence anisotropy experiments: probing protein dynamics. Biophys J (2005) 1.21

Differential peptide dynamics is linked to major histocompatibility complex polymorphism. J Biol Chem (2004) 1.19

Collective Langevin dynamics of conformational motions in proteins. J Chem Phys (2006) 1.18

Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One (2011) 1.16

Aqueous urea solutions: structure, energetics, and urea aggregation. J Phys Chem B (2007) 1.16

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur Biophys J (2007) 1.14

Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci U S A (2010) 1.13

Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J Biol Chem (2002) 1.13

Normal modes and essential dynamics. Methods Mol Biol (2008) 1.12

Can principal components yield a dimension reduced description of protein dynamics on long time scales? J Phys Chem B (2006) 1.12

Quantitative structural analysis of importin-β flexibility: paradigm for solenoid protein structures. Structure (2010) 1.11

Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J Mol Biol (2008) 1.09

Mechanical properties of single motor molecules studied by three-dimensional thermal force probing in optical tweezers. Chemphyschem (2004) 1.09

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput (2011) 1.09

Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. Biophys J (2007) 1.07

Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl (2011) 1.07

Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and absorption spectra. Angew Chem Int Ed Engl (2007) 1.06

Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain. Mol Biol Cell (2005) 1.06

Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. Biophys J (2009) 1.06

Influenza virus binds its host cell using multiple dynamic interactions. Proc Natl Acad Sci U S A (2012) 1.05

Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice. J Biol Chem (2011) 1.04

Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Comput Biol (2012) 1.04

β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure (2012) 1.04

Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc (2007) 1.04

Torsional elasticity and energetics of F1-ATPase. Proc Natl Acad Sci U S A (2011) 1.03

The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. Structure (2008) 1.03

Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J Am Chem Soc (2007) 1.02

Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handb Exp Pharmacol (2009) 1.02

An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins. Biophys J (2010) 1.02

Voltage-regulated water flux through aquaporin channels in silico. Biophys J (2010) 1.01

Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol (2010) 1.01

Determinants of water permeability through nanoscopic hydrophilic channels. Biophys J (2009) 1.01

Kinase-activity-independent functions of atypical protein kinase C in Drosophila. J Cell Sci (2009) 1.00

Molecular driving forces defining lipid positions around aquaporin-0. Proc Natl Acad Sci U S A (2012) 0.99

Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron. J Biol Chem (2010) 0.99

Polar or apolar--the role of polarity for urea-induced protein denaturation. PLoS Comput Biol (2008) 0.99

Structural basis for cooperativity of CRM1 export complex formation. Proc Natl Acad Sci U S A (2012) 0.98

Position of transmembrane helix 6 determines receptor G protein coupling specificity. J Am Chem Soc (2014) 0.98

Fluctuations of primary ubiquitin folding intermediates in a force clamp. J Struct Biol (2006) 0.98

Mechanical coupling via the membrane fusion SNARE protein syntaxin 1A: a molecular dynamics study. Biophys J (2003) 0.97

Flooding in GROMACS: accelerated barrier crossings in molecular dynamics. J Comput Chem (2006) 0.97