Published in J Chem Inf Model on March 19, 2008
Ethanol's molecular targets. Sci Signal (2008) 2.06
Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation. Proc Natl Acad Sci U S A (2013) 1.32
Alcohol-binding sites in distinct brain proteins: the quest for atomic level resolution. Alcohol Clin Exp Res (2011) 0.99
Alcohol dependence: molecular and behavioral evidence. Trends Pharmacol Sci (2014) 0.96
Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics. Pharmacol Rev (2014) 0.90
Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor. Anesthesiology (2013) 0.90
Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model. ACS Chem Neurosci (2010) 0.79
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
Emerging molecular mechanisms of general anesthetic action. Trends Pharmacol Sci (2005) 2.91
Coupling of agonist binding to channel gating in the GABA(A) receptor. Nature (2003) 2.89
Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55
Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophys J (2003) 2.38
Ethanol's molecular targets. Sci Signal (2008) 2.06
Simulations of the role of water in the protein-folding mechanism. Proc Natl Acad Sci U S A (2004) 1.95
An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. J Gen Physiol (2012) 1.72
Improved model quality assessment using ProQ2. BMC Bioinformatics (2012) 1.70
Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci (2008) 1.56
Structural basis for alcohol modulation of a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A (2011) 1.52
Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel. PLoS Comput Biol (2009) 1.51
Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci U S A (2012) 1.46
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res (2006) 1.45
Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor. Biophys J (2011) 1.42
Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature (2012) 1.42
Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput Biol (2010) 1.42
3D pressure field in lipid membranes and membrane-protein complexes. Phys Rev Lett (2009) 1.30
Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state. Science (2013) 1.28
Evidence that ethanol acts on a target in Loop 2 of the extracellular domain of alpha1 glycine receptors. J Neurochem (2007) 1.26
Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophys J (2006) 1.24
Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23
Membrane proteins diffuse as dynamic complexes with lipids. J Am Chem Soc (2010) 1.21
Protein contents in biological membranes can explain abnormal solvation of charged and polar residues. Proc Natl Acad Sci U S A (2009) 1.18
Charged residues in the beta2 subunit involved in GABAA receptor activation. J Biol Chem (2003) 1.18
Loop 2 structure in glycine and GABA(A) receptors plays a key role in determining ethanol sensitivity. J Biol Chem (2009) 1.16
The role of lipid composition for insertion and stabilization of amino acids in membranes. J Chem Phys (2009) 1.15
Sites of excitatory and inhibitory actions of alcohols on neuronal alpha2beta4 nicotinic acetylcholine receptors. J Pharmacol Exp Ther (2003) 1.14
The common chemical motifs within anesthetic binding sites. Anesth Analg (2007) 1.13
3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state. Biophys J (2011) 1.11
A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling. J Comput Chem (2010) 1.10
Channel gating of the glycine receptor changes accessibility to residues implicated in receptor potentiation by alcohols and anesthetics. J Biol Chem (2004) 1.10
Model quality assessment for membrane proteins. Bioinformatics (2010) 1.10
A novel hyperekplexia-causing mutation in the pre-transmembrane segment 1 of the human glycine receptor alpha1 subunit reduces membrane expression and impairs gating by agonists. J Biol Chem (2004) 1.09
Tryptophan scanning mutagenesis in TM4 of the GABA(A) receptor alpha1 subunit: implications for modulation by inhaled anesthetics and ion channel structure. Neuropharmacology (2002) 1.08
Accessibility to residues in transmembrane segment four of the glycine receptor. Neuropharmacology (2005) 1.08
Cross-linking of sites involved with alcohol action between transmembrane segments 1 and 3 of the glycine receptor following activation. J Neurochem (2007) 1.08
Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4. J Chem Inf Model (2010) 1.05
Molecular targets and mechanisms for ethanol action in glycine receptors. Pharmacol Ther (2010) 1.03
General anesthetics have additive actions on three ligand gated ion channels. Anesth Analg (2008) 1.03
Endothelial fate mapping in mice with pulmonary hypertension. Circulation (2013) 1.02
Targets for ethanol action and antagonism in loop 2 of the extracellular domain of glycine receptors. J Neurochem (2008) 1.02
Ivermectin antagonizes ethanol inhibition in purinergic P2X4 receptors. J Pharmacol Exp Ther (2010) 1.01
Homology modeling of a human glycine alpha 1 receptor reveals a plausible anesthetic binding site. J Chem Inf Model (2005) 1.01
Anesthetic and ethanol effects on spontaneously opening glycine receptor channels. J Neurochem (2002) 1.00
Characterization of two mutations, M287L and Q266I, in the α1 glycine receptor subunit that modify sensitivity to alcohols. J Pharmacol Exp Ther (2011) 0.99
Zinc enhances ethanol modulation of the alpha1 glycine receptor. Neuropharmacology (2009) 0.99
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins (2008) 0.99
Alcohol-binding sites in distinct brain proteins: the quest for atomic level resolution. Alcohol Clin Exp Res (2011) 0.99
Titratable amino acid solvation in lipid membranes as a function of protonation state. J Phys Chem B (2009) 0.98
Cross-linking of glycine receptor transmembrane segments two and three alters coupling of ligand binding with channel opening. J Neurochem (2004) 0.97
Normal-mode analysis of the glycine alpha1 receptor by three separate methods. J Chem Inf Model (2007) 0.96
Multiple sites of ethanol action in alpha1 and alpha2 glycine receptors suggested by sensitivity to pressure antagonism. J Neurochem (2004) 0.95
Molecular mechanism for the dual alcohol modulation of Cys-loop receptors. PLoS Comput Biol (2012) 0.95
A transmembrane amino acid in the GABAA receptor β2 subunit critical for the actions of alcohols and anesthetics. J Pharmacol Exp Ther (2010) 0.94
Ethanol potentiation of glycine receptors expressed in Xenopus oocytes antagonized by increased atmospheric pressure. Alcohol Clin Exp Res (2003) 0.94
Disruption of an intersubunit electrostatic bond is a critical step in glycine receptor activation. Proc Natl Acad Sci U S A (2010) 0.93
Evaluation of a proposed mechanism of ligand-gated ion channel activation in the GABAA and glycine receptors. Neurosci Lett (2004) 0.93
Alanine-scanning mutagenesis in the signature disulfide loop of the glycine receptor alpha 1 subunit: critical residues for activation and modulation. Biochemistry (2004) 0.93
Roles for loop 2 residues of alpha1 glycine receptors in agonist activation. J Biol Chem (2008) 0.90
Charge and geometry of residues in the loop 2 β hairpin differentially affect agonist and ethanol sensitivity in glycine receptors. J Pharmacol Exp Ther (2012) 0.90
Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics. Pharmacol Rev (2014) 0.90
Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor. Anesthesiology (2013) 0.90
Stabilization of the GluCl ligand-gated ion channel in the presence and absence of ivermectin. Biophys J (2013) 0.90
Molecular mechanisms and binding site location for the noncompetitive antagonist crystal violet on nicotinic acetylcholine receptors. Biochemistry (2006) 0.89
Are sobriety and consciousness determined by water in protein cavities? Alcohol Clin Exp Res (2004) 0.89
Structure and dynamics of interfacial water in an Lalpha phase lipid bilayer from molecular dynamics simulations. Biophys J (2003) 0.88
Noncompetitive antagonist binding sites in the torpedo nicotinic acetylcholine receptor ion channel. Structure-activity relationship studies using adamantane derivatives. Biochemistry (2003) 0.88
GABA(A) receptor transmembrane amino acids are critical for alcohol action: disulfide cross-linking and alkyl methanethiosulfonate labeling reveal relative location of binding sites. J Neurochem (2013) 0.88
Structural models of ligand-gated ion channels: sites of action for anesthetics and ethanol. Alcohol Clin Exp Res (2013) 0.88
Mutation of a zinc-binding residue in the glycine receptor α1 subunit changes ethanol sensitivity in vitro and alcohol consumption in vivo. J Pharmacol Exp Ther (2012) 0.86
Zinc-dependent modulation of α2- and α3-glycine receptor subunits by ethanol. Alcohol Clin Exp Res (2013) 0.85
Water ordering at membrane interfaces controls fusion dynamics. J Am Chem Soc (2011) 0.85
The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain. PLoS One (2012) 0.85
Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sites. Structure (2013) 0.85
The conserved phenylalanine in the K+ channel voltage-sensor domain creates a barrier with unidirectional effects. Biophys J (2013) 0.84
Unique general anesthetic binding sites within distinct conformational states of the nicotinic acetylcholine receptor. Int Rev Neurobiol (2003) 0.84
Identifying the binding site(s) for antidepressants on the Torpedo nicotinic acetylcholine receptor: [3H]2-azidoimipramine photolabeling and molecular dynamics studies. Biochim Biophys Acta (2008) 0.84
The TM2 6' position of GABA(A) receptors mediates alcohol inhibition. J Pharmacol Exp Ther (2011) 0.82
Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels. Mol Pharmacol (2013) 0.81
Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane. J Am Chem Soc (2013) 0.80
Coupled diffusion in lipid bilayers upon close approach. J Am Chem Soc (2015) 0.80
Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions. Chem Phys Lipids (2013) 0.80
Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model. ACS Chem Neurosci (2010) 0.79
Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci (2010) 0.78
Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. J Phys Chem B (2014) 0.78
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J Comput Chem (2013) 0.78
The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology. Mol Membr Biol (2012) 0.77
Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. ChemMedChem (2012) 0.77