Published in J Phys Chem A on October 03, 2007
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. J Mol Biol (2008) 1.07
Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. J Chem Theory Comput (2008) 1.03
Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput (2014) 0.99
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A (2008) 0.98
The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state. J Phys Chem A (2009) 0.94
Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. J Phys Chem B (2010) 0.92
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions. J Chem Theory Comput (2014) 0.87
Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J Chem Theory Comput (2014) 0.87
Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase. Biophys J (2011) 0.86
Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra. J Am Chem Soc (2011) 0.85
Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc (2013) 0.84
Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc (2009) 0.84
Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev (2016) 0.84
A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions. J Chem Theory Comput (2012) 0.83
Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations. J Chem Phys (2010) 0.83
Extended polarization in third-order SCC-DFTB from chemical-potential equalization. J Phys Chem A (2012) 0.83
Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci (2015) 0.83
An implicit solvent model for SCC-DFTB with Charge-Dependent Radii. J Chem Theory Comput (2010) 0.81
Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B (2014) 0.80
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tables. J Chem Phys (2008) 0.80
Density-functional expansion methods: generalization of the auxiliary basis. J Chem Phys (2011) 0.79
Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J (2015) 0.79
DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput (2015) 0.78
Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry. J Comput Chem (2015) 0.77
A delocalized proton-binding site within a membrane protein. Biophys J (2014) 0.76
Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids. J Chem Theory Comput (2014) 0.75
VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions. J Chem Phys (2016) 0.75
Density-functional expansion methods: Grand challenges. Theor Chem Acc (2012) 0.75
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol (2004) 7.38
Conversion of channelrhodopsin into a light-gated chloride channel. Science (2014) 2.56
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26
Protein structural variation in computational models and crystallographic data. Structure (2007) 2.13
Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev (2013) 1.93
A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure (2002) 1.84
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins (2006) 1.67
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J (2006) 1.62
Heparanase expression in gallbladder carcinoma and its correlation to prognosis. J Gastroenterol Hepatol (2007) 1.48
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry (2008) 1.45
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc (2006) 1.43
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Comput Biol (2006) 1.39
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 1.36
An in silico analysis of dynamic changes in microRNA expression profiles in stepwise development of nasopharyngeal carcinoma. BMC Med Genomics (2012) 1.36
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. J Comput Chem (2003) 1.35
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys (2005) 1.33
pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. J Phys Chem B (2008) 1.32
Application of elastic network models to proteins in the crystalline state. Biophys J (2009) 1.30
Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A (2007) 1.27
pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B (2005) 1.23
Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry (2004) 1.22
Ion selectivity in channels and transporters. J Gen Physiol (2011) 1.22
Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase. Biophys J (2004) 1.21
Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels. Assay Drug Dev Technol (2010) 1.20
A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J (2006) 1.20
Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations. Biophys J (2008) 1.18
What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc (2003) 1.18
Mechanism of primary proton transfer in bacteriorhodopsin. Structure (2004) 1.17
Importance of van der Waals Interactions in QM/MM Simulations. J Phys Chem B (2004) 1.16
Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies. J Am Chem Soc (2007) 1.14
Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J (2005) 1.14
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun (2013) 1.10
Many local motions cooperate to produce the adenylate kinase conformational transition. J Mol Biol (2010) 1.10
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc (2006) 1.09
Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. J Phys Chem A (2007) 1.09
Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. PLoS Comput Biol (2006) 1.08
Interpreting correlated motions using normal mode analysis. Structure (2006) 1.08
Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. J Mol Biol (2008) 1.07
Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model. Biochemistry (2009) 1.07
Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II. J Am Chem Soc (2003) 1.06
Activation mechanism of a signaling protein at atomic resolution from advanced computations. J Am Chem Soc (2007) 1.06
Selective inhibition of the K(ir)2 family of inward rectifier potassium channels by a small molecule probe: the discovery, SAR, and pharmacological characterization of ML133. ACS Chem Biol (2011) 1.06
Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations. Biophys J (2009) 1.05
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Phys Chem Chem Phys (2005) 1.04
Modulation of hERG potassium channel gating normalizes action potential duration prolonged by dysfunctional KCNQ1 potassium channel. Proc Natl Acad Sci U S A (2012) 1.03
Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. J Chem Theory Comput (2008) 1.03
Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework. Biophys J (2008) 1.01
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications. J Phys Chem A (2007) 1.00
On the utilization of energy minimization to the study of ion selectivity. Biophys J (2009) 0.99
Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data. J Chem Phys (2005) 0.98
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A (2008) 0.98
Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angew Chem Int Ed Engl (2003) 0.97
Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. Biochim Biophys Acta (2009) 0.97
A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability. Biophys J (2009) 0.96
Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. J Am Chem Soc (2005) 0.96
The Discovery and Characterization of ML218: A Novel, Centrally Active T-Type Calcium Channel Inhibitor with Robust Effects in STN Neurons and in a Rodent Model of Parkinson's Disease. ACS Chem Neurosci (2011) 0.96
Spectroscopic properties of tyrosyl radicals in dipeptides. J Am Chem Soc (2002) 0.94
The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state. J Phys Chem A (2009) 0.94
11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry (2002) 0.94
Two-photon fluorescence and second-harmonic generation imaging of collagen in human tissue based on multiphoton microscopy. Scanning (2011) 0.93
Automatized parametrization of SCC-DFTB repulsive potentials: application to hydrocarbons. J Phys Chem A (2009) 0.93
Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations. Proc Natl Acad Sci U S A (2010) 0.92
Nonadiabatic QM/MM simulations of fast charge transfer in Escherichia coli DNA photolyase. J Phys Chem B (2011) 0.92
Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. J Am Chem Soc (2002) 0.92
Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering. Biophys J (2010) 0.92
Treatment of cancer with a novel dual-targeted conditionally replicative adenovirus armed with mda-7/IL-24 gene. Clin Cancer Res (2008) 0.92
Reduction of imines by hydroxycyclopentadienyl ruthenium hydride: intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. J Am Chem Soc (2005) 0.91
What governs the charge transfer in DNA? The role of DNA conformation and environment. J Phys Chem B (2008) 0.91
Identification of (R)-N-(4-(4-methoxyphenyl)thiazol-2-yl)-1-tosylpiperidine-2-carboxamide, ML277, as a novel, potent and selective K(v)7.1 (KCNQ1) potassium channel activator. Bioorg Med Chem Lett (2012) 0.91
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discuss (2013) 0.90
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism. J Mol Biol (2013) 0.90
Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol. J Phys Chem B (2009) 0.90
Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89
Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment. J Phys Chem B (2006) 0.89
Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Proc Natl Acad Sci U S A (2013) 0.89
Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II. J Phys Chem B (2008) 0.89
Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study. J Phys Chem B (2009) 0.89
Identification of the Ah-receptor structural determinants for ligand preferences. Toxicol Sci (2012) 0.89
How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations. Langmuir (2010) 0.89
Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions. Biophys J (2008) 0.88