Published in J Phys Chem B on March 28, 2007
Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev (2014) 1.13
Charge transfer in dynamical biosystems, or the treachery of (static) images. Acc Chem Res (2014) 1.01
Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. Theochem (2009) 0.92
Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach. J Chem Phys (2008) 0.92
Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method. J Chem Phys (2009) 0.88
On the zwitterionic nature of gas-phase peptides and protein ions. PLoS Comput Biol (2010) 0.86
The molecular determinants of the increased reduction potential of the rubredoxin domain of rubrerythrin relative to rubredoxin. Biophys J (2010) 0.84
QM/MM molecular dynamics studies of metal binding proteins. Biomolecules (2014) 0.80
Dynamical magnetostructural properties of Anabaena ferredoxin. Proc Natl Acad Sci U S A (2007) 0.79
A hybrid approach to simulation of electron transfer in complex molecular systems. J R Soc Interface (2013) 0.78
Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru(2+)-Ru(3+) Self-Exchange Electron Transfer. J Chem Theory Comput (2012) 0.77
Performance comparison of computational methods for modeling alpha-helical structures. J Mol Model (2012) 0.76
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV. J Biol Inorg Chem (2007) 0.76
Triggering dynamics of the high-pressure benzene amorphization. Nat Mater (2006) 1.66
Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci (2002) 1.54
Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins (2004) 1.51
Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proc Natl Acad Sci U S A (2008) 1.25
The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site. J Biol Chem (2007) 1.23
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J Mol Biol (2002) 1.22
Targeting biomolecular flexibility with metadynamics. Curr Opin Struct Biol (2010) 1.16
Polarization effects and charge transfer in the KcsA potassium channel. Biophys Chem (2006) 1.12
Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor. PLoS One (2010) 1.12
Solute-solvent charge transfer in aqueous solution. Chemphyschem (2005) 1.04
Potassium permeation through the KcsA channel: a density functional study. Biochim Biophys Acta (2002) 1.04
Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction. J Am Chem Soc (2004) 1.03
Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. J Am Chem Soc (2005) 1.03
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc (2009) 1.02
A structural model of agonist binding to the alpha3beta4 neuronal nicotinic receptor. Br J Pharmacol (2003) 1.02
Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys Rev Lett (2005) 1.02
The C-terminal Src inhibitory kinase (Csk)-mediated tyrosine phosphorylation is a novel molecular mechanism to limit P2X3 receptor function in mouse sensory neurons. J Biol Chem (2009) 1.00
Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A (2006) 1.00
Structural facets of disease-linked human prion protein mutants: a molecular dynamic study. Proteins (2010) 0.97
Convergent dynamics in the protease enzymatic superfamily. J Am Chem Soc (2006) 0.97
On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson Disease. A combined computational and in vitro study. J Biol Chem (2007) 0.97
Dynamics and energetics of water permeation through the aquaporin channel. Proteins (2004) 0.97
Moving protons with pendant amines: proton mobility in a nickel catalyst for oxidation of hydrogen. J Am Chem Soc (2011) 0.96
GOMoDo: A GPCRs online modeling and docking webserver. PLoS One (2013) 0.96
Inhibition of alpha-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region. PLoS One (2008) 0.95
The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J Chem Phys (2005) 0.94
Water-assisted reaction mechanism of monozinc beta-lactamases. J Am Chem Soc (2004) 0.94
Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. J Biol Chem (2009) 0.94
Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: implications for ion permeation. J Recept Signal Transduct Res (2002) 0.94
Dissociation of minor groove binders from DNA: insights from metadynamics simulations. Nucleic Acids Res (2008) 0.94
Isobaric-isothermal molecular dynamics simulations utilizing density functional theory: an assessment of the structure and density of water at near-ambient conditions. J Phys Chem B (2009) 0.93
Regulation of bestrophins by Ca2+: a theoretical and experimental study. PLoS One (2009) 0.93
Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. J Am Chem Soc (2007) 0.91
Hydrogen oxidation catalysis by a nickel diphosphine complex with pendant tert-butyl amines. Chem Commun (Camb) (2010) 0.89
Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein. Inorg Chem (2010) 0.89
Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. Biophys J (2010) 0.89
Molecular modeling of ion channels: structural predictions. Curr Opin Chem Biol (2003) 0.89
Diabatic free energy curves and coordination fluctuations for the aqueous Ag+Ag2+ redox couple: a biased Born-Oppenheimer molecular dynamics investigation. J Chem Phys (2006) 0.89
Common structural traits across pathogenic mutants of the human prion protein and their implications for familial prion diseases. J Mol Biol (2011) 0.89
Incorporating peptides in the outer-coordination sphere of bioinspired electrocatalysts for hydrogen production. Inorg Chem (2011) 0.88
Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. Chemistry (2007) 0.88
Peptide aptamers targeting mutant p53 induce apoptosis in tumor cells. Cancer Res (2008) 0.88
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion. Proc Natl Acad Sci U S A (2012) 0.88
Nicotine blocks the hyperpolarization-activated current Ih and severely impairs the oscillatory behavior of oriens-lacunosum moleculare interneurons. J Neurosci (2010) 0.88
G protein inactive and active forms investigated by simulation methods. Proteins (2009) 0.88
Target-related applications of first principles quantum chemical methods in drug design. Chem Rev (2006) 0.88
Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding. PLoS One (2013) 0.87
Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study. J Am Chem Soc (2002) 0.87
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struct Biol (2007) 0.87
Ab initio molecular dynamics for molecules with variable numbers of electrons. Phys Rev Lett (2002) 0.87
Alignment of electronic energy levels at electrochemical interfaces. Phys Chem Chem Phys (2012) 0.87
Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes. J Chem Phys (2005) 0.87
Molecular dynamics study of the KcsA channel at 2.0-A resolution: stability and concerted motions within the pore. Biochim Biophys Acta (2004) 0.87
Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One (2012) 0.86
Ab initio molecular dynamics using hybrid density functionals. J Chem Phys (2008) 0.86
Origin of functional diversity among tetrameric voltage-gated channels. Proteins (2007) 0.86
QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. Chemphyschem (2003) 0.86
On the zwitterionic nature of gas-phase peptides and protein ions. PLoS Comput Biol (2010) 0.86
Mechanism of action of cyclophilin a explored by metadynamics simulations. PLoS Comput Biol (2009) 0.86
Calcium binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase: insights from molecular modeling. Proteins (2003) 0.85
Ligand specificity of odorant receptors. J Mol Model (2006) 0.85
Synthesis of two-dimensional analogues of copolymers by site-to-site transmetalation of organometallic monolayer sheets. J Am Chem Soc (2014) 0.85
Discovery of a class of diketopiperazines as antiprion compounds. ChemMedChem (2010) 0.84
Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus. Proteins (2004) 0.84
Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site. J Biol Inorg Chem (2002) 0.84
A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts. Biochemistry (2013) 0.84
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations. Biophys J (2006) 0.84
Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation. J Phys Chem B (2006) 0.84
Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics. J Chem Phys (2009) 0.83
Microseconds dynamics simulations of the outer-membrane protease T. Biophys J (2007) 0.83
Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations. J Phys Chem B (2006) 0.83
Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des (2011) 0.83
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins (2008) 0.83
Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction: the Marcus perspective. J Phys Chem B (2005) 0.83
A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations. J Phys Chem B (2012) 0.83
Structural basis of gating of CNG channels. FEBS Lett (2005) 0.83
Anthramycin-DNA binding explored by molecular simulations. J Phys Chem B (2006) 0.83
Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations. FEBS Lett (2011) 0.82
Computational molecular biology approaches to ligand-target interactions. HFSP J (2009) 0.82
Oxide/water interfaces: how the surface chemistry modifies interfacial water properties. J Phys Condens Matter (2012) 0.82
Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A. Biophys J (2006) 0.82
Structural role of compensatory amino acid replacements in the α-synuclein protein. Biochemistry (2011) 0.82
Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex. Proteins (2006) 0.82
A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. J Am Chem Soc (2004) 0.82
Comparative analysis of HIV-1 Tat variants. Proteins (2005) 0.82
Design of human granzyme B variants resistant to serpin B9. Proteins (2012) 0.82
Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase. Biochim Biophys Acta (2013) 0.81
Ab initio molecular dynamics simulation of a medium-sized water cluster anion: from an interior to a surface-located excess electron via a delocalized state. J Phys Chem A (2008) 0.81
Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study. J Phys Chem B (2012) 0.81
Conformational fluctuations of UreG, an intrinsically disordered enzyme. Biochemistry (2013) 0.81
Dielectric properties of water ice, the ice Ih/XI phase transition, and an assessment of density functional theory. J Phys Chem B (2014) 0.81
Electronic structure of wet DNA. Phys Rev Lett (2002) 0.81
Modulation of alpha-synuclein aggregation by dopamine analogs. PLoS One (2010) 0.81
Structure/function relationships of phospholipases C Beta. Curr Protein Pept Sci (2013) 0.80
Platination of the copper transporter ATP7A involved in anticancer drug resistance. Dalton Trans (2014) 0.80