Published in Biophys J on November 01, 2002
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Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. Biophys J (2004) 1.55
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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
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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
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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
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
Docking of mu-conotoxin GIIIA in the sodium channel outer vestibule. Channels (Austin) (2007) 1.07
Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 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
The TatA subunit of Escherichia coli twin-arginine translocase has an N-in topology. Biochemistry (2007) 1.02
P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK. FEBS Lett (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
Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD. Biophys J (2007) 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
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
Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF. Biochemistry (2006) 0.89
Direct simulation of protein-mediated vesicle fusion: lung surfactant protein B. Biophys J (2010) 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
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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
Residue G346 in transmembrane segment six is involved in inter-domain communication in P-glycoprotein. Biochemistry (2007) 0.84
Computer simulations of the phase separation in model membranes. Faraday Discuss (2013) 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
Molecular structure of membrane tethers. Biophys J (2012) 0.82
The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations. Soft Matter (2014) 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
Holo-BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD. Proteins (2010) 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
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
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
Molecular dynamics simulations of beta-ketoacyl-, beta-hydroxyacyl-, and trans-2-enoyl-acyl carrier proteins of Escherichia coli. Biochemistry (2010) 0.80
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
The importance of membrane defects-lessons from simulations. Acc Chem Res (2014) 0.79
Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors. J Am Chem Soc (2005) 0.79
The distribution and conformation of very long-chain plant wax components in a lipid bilayer. J Phys Chem B (2007) 0.79
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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
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
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
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