Published in Curr Opin Struct Biol on January 29, 2010
Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins (2005) 1.74
Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys J (2004) 1.40
Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys J (2005) 1.19
A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophys J (2007) 1.15
Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins (2004) 1.09
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc Natl Acad Sci U S A (2007) 1.07
Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations. J Phys Chem B (2006) 1.01
Molecular dynamics simulation of deoxy and carboxy murine neuroglobin in water. Biophys J (2007) 0.96
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A (2011) 0.96
Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc (2009) 0.95
Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys J (2005) 0.94
Misfolding of the amyloid beta-protein: a molecular dynamics study. Proteins (2006) 0.94
Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin. Proteins (2002) 0.93
Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys J (2003) 0.92
Gold-catalyzed reactions of 2-alkynyl-phenylamines with alpha,beta-enones. J Org Chem (2005) 0.91
Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water. Proteins (2005) 0.90
The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations. Biophys J (2008) 0.90
Charge-based interactions between peptides observed as the dominant force for association in aqueous solution. Angew Chem Int Ed Engl (2008) 0.89
Natural D240G Toho-1 mutant conferring resistance to ceftazidime: biochemical characterization of CTX-M-43. J Antimicrob Chemother (2008) 0.88
Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water. Proteins (2005) 0.88
Global and local motions in ribonuclease A: a molecular dynamics study. Biopolymers (2002) 0.88
Subdiffusion in peptides originates from the fractal-like structure of configuration space. Phys Rev Lett (2008) 0.87
Molecular dynamics simulations of lignin peroxidase in solution. Biophys J (2003) 0.85
Design, modelling, synthesis and biological evaluation of peptidomimetic phosphinates as inhibitors of matrix metalloproteinases MMP-2 and MMP-8. Bioorg Med Chem (2005) 0.85
Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics. J Comput Aided Mol Des (2005) 0.85
Folding propensity and biological activity of peptides: the effect of a single stereochemical isomerization on the conformational properties of bombinins in aqueous solution. Biopolymers (2008) 0.84
Theoretical characterization of carbon monoxide vibrational spectrum in sperm whale myoglobin distal pocket. Biophys J (2007) 0.84
Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution. Biophys J (2008) 0.83
The reversible opening of water channels in cytochrome c modulates the heme iron reduction potential. J Am Chem Soc (2012) 0.83
The role of arginine 38 in horseradish peroxidase enzyme revisited: a computational investigation. Biophys Chem (2009) 0.83
Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins (2007) 0.83
Dynamic investigation of protein metal active sites: interplay of XANES and molecular dynamics simulations. J Am Chem Soc (2010) 0.82
Theoretical characterization of alpha-helix and beta-hairpin folding kinetics. J Am Chem Soc (2005) 0.81
Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor. J Comput Aided Mol Des (2002) 0.81
Structural insight into peroxisome proliferator-activated receptor gamma binding of two ureidofibrate-like enantiomers by molecular dynamics, cofactor interaction analysis, and site-directed mutagenesis. J Med Chem (2010) 0.80
Mechanism of DNA recognition by the restriction enzyme EcoRV. J Mol Biol (2010) 0.80
Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa. Proteins (2003) 0.80
Conformational fluctuations and electronic properties in myoglobin. J Comput Chem (2004) 0.79
Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophys J (2011) 0.79
Molecular dynamics simulation of Leishmania major surface metalloprotease GP63 (leishmanolysin). Proteins (2006) 0.79
Free-energy profile for CO binding to separated chains of human and Trematomus newnesi hemoglobin: insights from molecular dynamics simulations and perturbed matrix method. J Phys Chem B (2010) 0.79
Conformational analysis and UV/Vis spectroscopic properties of a rotaxane-based molecular machine in acetonitrile dilute solution: when simulations meet experiments. Phys Chem Chem Phys (2010) 0.78
Role of the amino sugar in the DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG). Bioorg Med Chem (2005) 0.78
Kinetics of carbon monoxide migration and binding in solvated neuroglobin as revealed by molecular dynamics simulations and quantum mechanical calculations. J Phys Chem B (2011) 0.78
Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. PLoS Comput Biol (2011) 0.78
Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase. J Phys Chem B (2008) 0.78
Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations. J Phys Chem B (2009) 0.78
Computational study of the reaction of N(2D) atoms with CH2F radicals: an example of a barrier-free reaction involving very high internal energies. J Chem Phys (2005) 0.78
Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations. J Am Chem Soc (2012) 0.77
Cyclochiral resorcin[4]arenes as effective enantioselectors in the gas phase. J Mass Spectrom (2012) 0.77
Modeling of chemical reactions in micelle: water-mediated keto-enol interconversion as a case study. J Phys Chem B (2011) 0.77
Simulation of the amide I infrared spectrum in photoinduced peptide folding/unfolding transitions. J Phys Chem B (2013) 0.77
An integrated computational approach to rationalize the activity of non-zinc-binding MMP-2 inhibitors. PLoS One (2012) 0.77
Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case. J Chem Phys (2005) 0.77
Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study. J Chem Phys (2005) 0.77
The effect of protein conformational flexibility on the electronic properties of a chromophore. Biophys J (2003) 0.77
Theoretical study of alpha-84 phycocyanobilin chromophore from the thermophilic cyanobacterium Synechococcus elongatus. J Phys Chem B (2007) 0.77
Peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt): conformation of Boc-Adt-Adt-NHMe and NH...S interactions. J Pept Sci (2005) 0.77
A mean field approach for molecular simulations of fluid systems. J Chem Phys (2005) 0.77
Conformational and electronic properties of a microperoxidase in aqueous solution: a computational study. Chemphyschem (2005) 0.77
A few key residues determine the high redox potential shift in azurin mutants. Org Biomol Chem (2015) 0.76
Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. J Phys Chem B (2008) 0.76
Structural and dynamical properties of KTS-disintegrins: A comparison between Obtustatin and Lebestatin. Biopolymers (2013) 0.76
Structural modifications of ionic liquid surfactants for improving the water dispersibility of carbon nanotubes: an experimental and theoretical study. Phys Chem Chem Phys (2011) 0.76
Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism. Biometals (2010) 0.76
Surface packing determines the redox potential shift of cytochrome c adsorbed on gold. J Am Chem Soc (2014) 0.76
Structure-Activity Relationship of novel phenylacetic CXCR1 inhibitors. Bioorg Med Chem Lett (2009) 0.76
Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Protein Sci (2004) 0.76
Aggregation of small peptides studied by molecular dynamics simulations. Proteins (2006) 0.76
The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations. Proteins (2010) 0.76
New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide. J Am Chem Soc (2011) 0.75
Instantaneous normal modes and the protein glass transition. Biophys J (2009) 0.75
Liposome destabilization by a 2,7-diazapyrenium derivative through formation of transient pores in the lipid bilayer. Small (2010) 0.75
Configurational subdiffusion of peptides: a network study. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Computational study on compound I redox-active species in horseradish peroxydase enzyme: conformational fluctuations and solvation effects. J Phys Chem B (2010) 0.75
A theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra. J Phys Chem B (2012) 0.75
Theoretical characterization of electronic states in interacting chemical systems. J Chem Phys (2009) 0.75
A general theoretical model for electron transfer reactions in complex systems. Phys Chem Chem Phys (2011) 0.75
Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: comparison with recent experimental data. J Chem Phys (2008) 0.75
Charge transfer equilibria of aqueous single stranded DNA. Phys Chem Chem Phys (2009) 0.75
Fast stereoselective reactions in electrosprayed Co(II)/neurotransmitter nanodroplets. Chem Commun (Camb) (2008) 0.75
A fast redox-induced switching mechanism in a conformationally controllable molecular thread in solution. Phys Chem Chem Phys (2010) 0.75
On the structural affinity of macromolecules with different biological properties: molecular dynamics simulations of a series of TEM-1 mutants. Biochem Biophys Res Commun (2013) 0.75
Can a synthetic thread act as an electrochemically switchable molecular device? Chem Commun (Camb) (2008) 0.75
P-113 Peptide: New experimental evidences on its biological activity and conformational insights from molecular dynamics simulations. Biopolymers (2014) 0.75
Analysis of infrared spectra of β-hairpin peptides as derived from molecular dynamics simulations. J Phys Chem B (2011) 0.75