Published in J Am Chem Soc on September 19, 2007
A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06
Ras trafficking, localization and compartmentalized signalling. Semin Cell Dev Biol (2011) 1.48
Novel allosteric sites on Ras for lead generation. PLoS One (2011) 1.20
Staurosporines disrupt phosphatidylserine trafficking and mislocalize Ras proteins. J Biol Chem (2012) 1.15
The C-terminal sequence of RhoB directs protein degradation through an endo-lysosomal pathway. PLoS One (2009) 0.99
Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect. Biophys J (2008) 0.95
Formation and domain partitioning of H-ras peptide nanoclusters: effects of peptide concentration and lipid composition. J Am Chem Soc (2012) 0.95
Nonsteroidal anti-inflammatory drugs alter the spatiotemporal organization of Ras proteins on the plasma membrane. J Biol Chem (2012) 0.94
Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras. Biophys J (2010) 0.90
The role of G-domain orientation and nucleotide state on the Ras isoform-specific membrane interaction. Eur Biophys J (2012) 0.90
GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site. J Biol Chem (2015) 0.90
Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation. J Am Chem Soc (2008) 0.88
Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. PLoS One (2013) 0.87
Lessons from computer simulations of Ras proteins in solution and in membrane. Biochim Biophys Acta (2013) 0.87
Identification of H-Ras-specific motif for the activation of invasive signaling program in human breast epithelial cells. Neoplasia (2011) 0.87
The C-terminus of H-Ras as a target for the covalent binding of reactive compounds modulating Ras-dependent pathways. PLoS One (2011) 0.86
Deformation of a Two-domain Lipid Bilayer due to Asymmetric Insertion of Lipid-modified Ras Peptides. Soft Matter (2013) 0.86
The higher level of complexity of K-Ras4B activation at the membrane. FASEB J (2015) 0.85
Thermodynamics of peptide insertion and aggregation in a lipid bilayer. J Phys Chem B (2008) 0.84
The peptide hormone ghrelin binds to membrane-mimetics via its octanoyl chain and an adjacent phenylalanine. Bioorg Med Chem (2010) 0.81
Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Chem Soc Rev (2016) 0.80
Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras. Mol Simul (2014) 0.79
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The Role of Signaling via Aqueous Pore Formation in Resistance Responses to Amphotericin B. Antimicrob Agents Chemother (2016) 0.76
AMPK and Endothelial Nitric Oxide Synthase Signaling Regulates K-Ras Plasma Membrane Interactions via Cyclic GMP-Dependent Protein Kinase 2. Mol Cell Biol (2016) 0.75
The Molecular Mechanism Underlying Recruitment and Insertion of Lipid-Anchored LC3 Protein into Membranes. Biophys J (2015) 0.75
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
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Antimicrobial peptides of multicellular organisms. Nature (2002) 23.50
An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science (2005) 5.99
Lipid rafts: contentious only from simplistic standpoints. Nat Rev Mol Cell Biol (2006) 4.94
GTP-dependent segregation of H-ras from lipid rafts is required for biological activity. Nat Cell Biol (2001) 4.42
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J (2000) 3.93
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Molecular mechanism of antimicrobial peptides: the origin of cooperativity. Biochim Biophys Acta (2006) 2.36
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Ras plasma membrane signalling platforms. Biochem J (2005) 2.15
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Three separable domains regulate GTP-dependent association of H-ras with the plasma membrane. Mol Cell Biol (2004) 2.09
Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation. Biophys J (2003) 1.99
Fluorimetric evaluation of the affinities of isoprenylated peptides for lipid bilayers. Biochemistry (1994) 1.99
Lipid rafts and plasma membrane microorganization: insights from Ras. Trends Cell Biol (2004) 1.92
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84
Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane. Mol Cell Biol (2006) 1.81
Membrane thinning due to antimicrobial peptide binding: an atomic force microscopy study of MSI-78 in lipid bilayers. Biophys J (2005) 1.81
New insights into the mechanisms of protein palmitoylation. Biochemistry (2003) 1.79
Energetics of pore formation induced by membrane active peptides. Biochemistry (2004) 1.77
Membrane thinning effect of the beta-sheet antimicrobial protegrin. Biochemistry (2000) 1.64
Peptide-membrane interactions and mechanisms of membrane destruction by amphipathic alpha-helical antimicrobial peptides. Biochim Biophys Acta (2006) 1.62
Ras nanoclusters: molecular structure and assembly. Semin Cell Dev Biol (2007) 1.56
The linker domain of the Ha-Ras hypervariable region regulates interactions with exchange factors, Raf-1 and phosphoinositide 3-kinase. J Biol Chem (2001) 1.44
Many-body effect of antimicrobial peptides: on the correlation between lipid's spontaneous curvature and pore formation. Biophys J (2005) 1.36
Assess the nature of cholesterol-lipid interactions through the chemical potential of cholesterol in phosphatidylcholine bilayers. Proc Natl Acad Sci U S A (2007) 1.31
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Ras signaling from plasma membrane and endomembrane microdomains. Biochim Biophys Acta (2005) 1.28
Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J Am Chem Soc (2004) 1.27
Mechanisms of Ras protein targeting in mammalian cells. J Membr Biol (2002) 1.27
Evidence of cholesterol accumulated in high curvature regions: implication to the curvature elastic energy for lipid mixtures. Biophys J (2007) 1.20
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J (2006) 1.18
Self-induced docking site of a deeply embedded peripheral membrane protein. Biophys J (2006) 1.14
Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy. J Am Chem Soc (2003) 1.12
Domain formation induced by the adsorption of charged proteins on mixed lipid membranes. Biophys J (2004) 1.12
Free energy profile of H-ras membrane anchor upon membrane insertion. Angew Chem Int Ed Engl (2007) 1.04
Perturbation of a lipid membrane by amphipathic peptides and its role in pore formation. Eur Biophys J (2004) 1.03
Site-specific deuterium order parameters and membrane-bound behavior of a peptide fragment from the intracellular domain of HIV-1 gp41. Biochemistry (1999) 1.03
Targeting and localized signalling by small GTPases. Biol Cell (2007) 0.98
Membrane perturbation induced by interfacially adsorbed peptides. Biophys J (2004) 0.98
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Peptide-lipid interactions and mechanisms of antimicrobial peptides. Novartis Found Symp (1999) 0.92
Insertion of lipidated Ras proteins into lipid monolayers studied by infrared reflection absorption spectroscopy (IRRAS). Biophys J (2006) 0.88
Multiple antigenic peptides facilitate generation of anti-prion antibodies. Clin Exp Immunol (2004) 0.81
Bridging the gap between cell biology and organic chemistry: chemical synthesis and biological application of lipidated peptides and proteins. Naturwissenschaften (2002) 0.81
The chemical biology of Ras lipidation. Biol Chem (2001) 0.78
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Normal cellular Ha ras p21 protein causes local disruption of bilayer phospholipid. Biochemistry (1988) 0.77
Synthesis of palmitoylated Ras-peptides and -proteins. Methods (2006) 0.77
Linking the fields--the interplay of organic synthesis, biophysical chemistry, and cell biology in the chemical biology of protein lipidation. Chembiochem (2000) 0.76
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53
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Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69
Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58
Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A (2006) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10
Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09
A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc (2004) 2.00
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys (2007) 1.93
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem (2004) 1.81
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80
POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model (2010) 1.75
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (2008) 1.75
Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys (2007) 1.73
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67
A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2005) 1.66
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65
Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol (2005) 1.64
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model (2008) 1.64
Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc (2002) 1.63
Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62
Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput (2008) 1.52
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc (2005) 1.51
Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol (2008) 1.51
Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B (2008) 1.45
How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput (2010) 1.44
Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov (2011) 1.44
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys (2007) 1.43
The physical basis of microtubule structure and stability. Protein Sci (2003) 1.43
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J (2006) 1.42
Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37
The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc (2006) 1.37
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res (2006) 1.37
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J (2004) 1.35
Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys (2011) 1.35
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A (2012) 1.33
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys (2005) 1.31
Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B (2005) 1.31
Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc (2005) 1.28
Molecular dynamics of acetylcholinesterase. Acc Chem Res (2002) 1.28
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J (2007) 1.28
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol (2009) 1.27
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol (2012) 1.26
Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A (2009) 1.25
Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem Biol Drug Des (2010) 1.24
Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. J Chem Theory Comput (2009) 1.23
Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol (2010) 1.23
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc (2005) 1.23
Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J (2003) 1.23
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys (2009) 1.22
Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. J Mol Biol (2009) 1.21
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model (2010) 1.21
Calculating pKa values in enzyme active sites. Protein Sci (2003) 1.21
Novel allosteric sites on Ras for lead generation. PLoS One (2011) 1.20
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J Am Chem Soc (2002) 1.20
Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J (2010) 1.20
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. J Am Chem Soc (2007) 1.19
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J Am Chem Soc (2005) 1.19
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J (2007) 1.18
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers (2004) 1.18
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc (2010) 1.18
Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J Am Chem Soc (2002) 1.17
Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J (2005) 1.17
Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol (2007) 1.17
Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys J (2003) 1.17
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol (2006) 1.17
On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci (2003) 1.17
Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc (2004) 1.16
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol (2011) 1.16
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc (2006) 1.15
Towards an in vivo biologically inspired nanofactory. Nat Nanotechnol (2007) 1.15
Structural and dynamic properties of water around acetylcholinesterase. Protein Sci (2002) 1.15
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry (2011) 1.14
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A (2007) 1.14
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14
Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B (2007) 1.14
Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers (2006) 1.14