Published in Biophys J on March 01, 2003
Lysine methylation strategies for characterizing protein conformations by NMR. J Biomol NMR (2012) 0.83
A thermodynamic approach to alamethicin pore formation. Biochim Biophys Acta (2013) 0.78
Ion permeation of pores in model membranes: selectivity, fluctuations and the role of surface charge. Eur Biophys J (2003) 0.75
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science (1998) 39.86
Raster3D: photorealistic molecular graphics. Methods Enzymol (1997) 27.30
X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity. Nature (2002) 9.96
Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science (1998) 7.51
Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct (1999) 4.81
The biophysics of peptide models of ion channels. Prog Biophys Mol Biol (1991) 2.59
A novel method for structure-based prediction of ion channel conductance properties. Biophys J (1997) 2.11
Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics. Biophys J (2000) 1.93
Simulation approaches to ion channel structure-function relationships. Q Rev Biophys (2001) 1.83
Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. Biochemistry (2001) 1.66
Electrostatics and the ion selectivity of ligand-gated channels. Biophys J (1998) 1.53
Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics. Biophys J (2000) 1.51
Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution. Structure (2000) 1.39
Theoretical and computational models of ion channels. Curr Opin Struct Biol (2002) 1.38
Analysis and evaluation of channel models: simulations of alamethicin. Biophys J (2002) 1.25
Intrinsic rectification of ion flux in alamethicin channels: studies with an alamethicin dimer. Biophys J (1997) 1.16
Engineering stabilized ion channels: covalent dimers of alamethicin. Biochemistry (1996) 1.10
Protonation of lysine residues inverts cation/anion selectivity in a model channel. Biophys J (2000) 0.88
An anion-selective analogue of the channel-forming peptide alamethicin. Biochemistry (1999) 0.87
Proline-induced distortions of transmembrane helices. J Mol Biol (2002) 2.76
Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1. Science (2010) 2.52
Liquid-vapor oscillations of water in hydrophobic nanopores. Proc Natl Acad Sci U S A (2003) 2.48
Acquisition of siderophores in gram-negative bacteria. Nat Rev Mol Cell Biol (2003) 2.24
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores. Phys Biol (2004) 2.13
Insertion and assembly of membrane proteins via simulation. J Am Chem Soc (2006) 2.12
Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J (2010) 2.05
H bonding at the helix-bundle crossing controls gating in Kir potassium channels. Neuron (2007) 2.02
Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure (2008) 1.98
Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J Struct Biol (2006) 1.91
Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol (2008) 1.86
Setting up and optimization of membrane protein simulations. Eur Biophys J (2002) 1.79
Functional analysis of a structural model of the ATP-binding site of the KATP channel Kir6.2 subunit. EMBO J (2005) 1.79
Azobenzene photoswitches for biomolecules. Chem Soc Rev (2011) 1.77
Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins (2005) 1.74
A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Phys Biol (2006) 1.70
3-D structural and functional characterization of the purified KATP channel complex Kir6.2-SUR1. EMBO J (2005) 1.66
Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc Natl Acad Sci U S A (2007) 1.59
The pore structure and gating mechanism of K2P channels. EMBO J (2011) 1.56
Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states. Proc Natl Acad Sci U S A (2013) 1.54
Molecular simulation approaches to membrane proteins. Structure (2011) 1.52
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry (2008) 1.51
Outer membrane protein G: Engineering a quiet pore for biosensing. Proc Natl Acad Sci U S A (2008) 1.48
Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer. J Mol Biol (2003) 1.47
How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure (2007) 1.46
Not ions alone: barriers to ion permeation in nanopores and channels. J Am Chem Soc (2004) 1.46
The structural basis of ZMPSTE24-dependent laminopathies. Science (2013) 1.43
K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study. Biophys J (2002) 1.42
Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis. EMBO J (2007) 1.41
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations. J Am Chem Soc (2010) 1.41
PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations. Biochemistry (2009) 1.40
Structural and functional analysis of the putative pH sensor in the Kir1.1 (ROMK) potassium channel. EMBO Rep (2006) 1.39
Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Comput Biol (2011) 1.37
Transmembrane helix prediction: a comparative evaluation and analysis. Protein Eng Des Sel (2005) 1.33
A gating mutation at the internal mouth of the Kir6.2 pore is associated with DEND syndrome. EMBO Rep (2005) 1.32
Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins (2004) 1.31
Viral ion channels: structure and function. Biochim Biophys Acta (2002) 1.31
Alpha-Helix folding in the presence of structural constraints. Proc Natl Acad Sci U S A (2008) 1.30
OmpA: a pore or not a pore? Simulation and modeling studies. Biophys J (2002) 1.28
Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues. J Gen Physiol (2008) 1.28
Azobenzene photoswitching without ultraviolet light. J Am Chem Soc (2011) 1.26
Analysis and evaluation of channel models: simulations of alamethicin. Biophys J (2002) 1.25
The selectivity of K+ ion channels: testing the hypotheses. Biophys J (2008) 1.24
Structure of the TatC core of the twin-arginine protein transport system. Nature (2012) 1.23
Identification of residues contributing to the ATP binding site of Kir6.2. EMBO J (2003) 1.22
Spectral tuning of azobenzene photoswitches for biological applications. Angew Chem Int Ed Engl (2009) 1.19
Multiscale methods for macromolecular simulations. Curr Opin Struct Biol (2008) 1.19
Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy. Proc Natl Acad Sci U S A (2005) 1.19
Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization. Biochemistry (2008) 1.18
Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA. Biophys J (2003) 1.18
Anionic phospholipid interactions with the potassium channel KcsA: simulation studies. Biophys J (2005) 1.18
Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol (2012) 1.18
Reduced lateral mobility of lipids and proteins in crowded membranes. PLoS Comput Biol (2013) 1.17
Ion channel gating: insights via molecular simulations. FEBS Lett (2003) 1.17
Filter flexibility in a mammalian K channel: models and simulations of Kir6.2 mutants. Biophys J (2003) 1.17
Control of pH and PIP2 gating in heteromeric Kir4.1/Kir5.1 channels by H-Bonding at the helix-bundle crossing. Channels (Austin) (2007) 1.17
Open-state models of a potassium channel. Biophys J (2002) 1.17
A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophys J (2007) 1.15
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study. Structure (2010) 1.14
Using an azobenzene cross-linker to either increase or decrease peptide helix content upon trans-to-cis photoisomerization. Chem Biol (2002) 1.14
Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies. Biopolymers (2002) 1.13
Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component. J Biol Chem (2006) 1.12
Photoswitching azo compounds in vivo with red light. J Am Chem Soc (2013) 1.12
Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics (2012) 1.12
Lipid-protein interactions of integral membrane proteins: a comparative simulation study. Biophys J (2004) 1.12
Increased ATPase activity produced by mutations at arginine-1380 in nucleotide-binding domain 2 of ABCC8 causes neonatal diabetes. Proc Natl Acad Sci U S A (2007) 1.11
Insight into the mechanism of inactivation and pH sensitivity in potassium channels from molecular dynamics simulations. Biochemistry (2008) 1.10
OmpA: gating and dynamics via molecular dynamics simulations. Biochim Biophys Acta (2007) 1.09
Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states. Biophys J (2003) 1.09
Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor. J Biol Chem (2006) 1.09
The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating. Biophys J (2005) 1.07
Potassium channel regulation. EMBO Rep (2003) 1.07
The simulation approach to bacterial outer membrane proteins. Mol Membr Biol (2004) 1.07
Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1. Biophys J (2004) 1.06
Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class. Biophys J (2011) 1.06
Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2. Biophys J (2002) 1.05
Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain. Structure (2011) 1.05
Conformational change in an MFS protein: MD simulations of LacY. Structure (2007) 1.05
Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components. Biochemistry (2007) 1.04
Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer. Biochemistry (2006) 1.04
A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore. J Biol Chem (2011) 1.04
Lipidbook: a public repository for force-field parameters used in membrane simulations. J Membr Biol (2010) 1.04
MD simulations of spontaneous membrane protein/detergent micelle formation. J Am Chem Soc (2004) 1.04
Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys J (2008) 1.03
Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. Acc Chem Res (2010) 1.03
Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett (2003) 1.02
Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces. Biophys J (2012) 1.02
Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling. PLoS Comput Biol (2011) 1.02
Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions. Biophys J (2005) 1.01
Stabilization of folded peptide and protein structures via distance matching with a long, rigid cross-linker. J Am Chem Soc (2007) 1.01
Structural model for the protein-translocating element of the twin-arginine transport system. Proc Natl Acad Sci U S A (2013) 1.01
Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment. J Phys Chem B (2005) 1.01
Structure-based approach to the photocontrol of protein folding. J Am Chem Soc (2009) 1.01
Lipid/protein interactions and the membrane/water interfacial region. J Am Chem Soc (2003) 1.01
Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis. Mol Membr Biol (2006) 1.00
Multiscale simulations suggest a mechanism for integrin inside-out activation. Proc Natl Acad Sci U S A (2011) 1.00
Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins. Structure (2013) 1.00
Focus on Kir6.2: a key component of the ATP-sensitive potassium channel. J Mol Cell Cardiol (2005) 1.00
Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA. Biophys J (2006) 1.00
OmpT: molecular dynamics simulations of an outer membrane enzyme. Biophys J (2004) 0.99