Published in J Comput Chem on April 15, 2003
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
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
Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. J Mol Biol (2008) 1.07
Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A (2006) 1.04
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
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations. Biochemistry (2008) 1.01
Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput (2014) 0.99
Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism. J Am Chem Soc (2009) 0.94
Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study. J Chem Theory Comput (2009) 0.94
Catalytic mechanism of aromatic prenylation by NphB. Biochemistry (2012) 0.91
QM/MM X-ray refinement of zinc metalloenzymes. J Inorg Biochem (2010) 0.89
Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc (2012) 0.86
Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. J Phys Chem A (2007) 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
Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2. J Phys Chem B (2011) 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
The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As. Biochemistry (2007) 0.82
An implicit solvent model for SCC-DFTB with Charge-Dependent Radii. J Chem Theory Comput (2010) 0.81
Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways. J Phys Chem B (2010) 0.81
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Density-functional expansion methods: generalization of the auxiliary basis. J Chem Phys (2011) 0.79
Quantum chemical study of silanediols as metal binding groups for metalloprotease inhibitors. J Mol Model (2013) 0.79
DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput (2015) 0.78
Strictly conserved lysine of prolyl-tRNA Synthetase editing domain facilitates binding and positioning of misacylated tRNA(Pro.). Biochemistry (2014) 0.78
A dynamic view of enzyme catalysis. J Mol Model (2008) 0.78
Inhibitor and substrate binding by angiotensin-converting enzyme: quantum mechanical/molecular mechanical molecular dynamics studies. J Chem Inf Model (2011) 0.75
Clarification of the mechanism of acylation reaction and origin of substrate specificity of the serine-carboxyl peptidase sedolisin through QM/MM free energy simulations. J Phys Chem B (2011) 0.75
pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis. J Phys Chem B (2011) 0.75
Metal Ion Modeling Using Classical Mechanics. Chem Rev (2017) 0.75
Intrinsic proton-donating power of zinc-bound water in a carbonic anhydrase active site model estimated by NMR. J Am Chem Soc (2011) 0.75
Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study. J Mol Model (2016) 0.75
Effect of mutation on the stabilization energy of HIV-1 zinc fingers: a hybrid local self-consistent field/molecular mechanics investigation. J Biol Inorg Chem (2016) 0.75
QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme. J Mol Model (2016) 0.75
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature (2007) 5.78
Intrinsic motions along an enzymatic reaction trajectory. Nature (2007) 5.53
How enzymes work: analysis by modern rate theory and computer simulations. Science (2004) 4.30
Allostery and cooperativity revisited. Protein Sci (2008) 3.70
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature (2005) 3.67
A Src-like inactive conformation in the abl tyrosine kinase domain. PLoS Biol (2006) 3.40
Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci U S A (2004) 2.65
Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J Mol Biol (2005) 2.59
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
Free energy simulations come of age: protein-ligand recognition. Acc Chem Res (2002) 2.04
Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol (2002) 2.00
Molecular dynamics simulations of biomolecules. Acc Chem Res (2002) 1.95
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol (2004) 1.92
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure (2010) 1.91
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
Melanin absorption spectroscopy: new method for noninvasive skin investigation and melanoma detection. J Biomed Opt (2008) 1.80
Graphene nanoFlakes with large spin. Nano Lett (2007) 1.73
Optimal estimates of free energies from multistate nonequilibrium work data. Phys Rev Lett (2006) 1.73
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins (2006) 1.67
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature (2009) 1.67
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J (2006) 1.62
Kinesin's cover-neck bundle folds forward to generate force. Proc Natl Acad Sci U S A (2008) 1.57
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell (2005) 1.55
Application of the diffusion-collision model to the folding of three-helix bundle proteins. J Mol Biol (2002) 1.53
Force generation in kinesin hinges on cover-neck bundle formation. Structure (2008) 1.53
Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc Natl Acad Sci U S A (2004) 1.52
The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G. Structure (2004) 1.51
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proc Natl Acad Sci U S A (2008) 1.50
New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B (2013) 1.48
Determination of a transition state at atomic resolution from protein engineering data. J Mol Biol (2002) 1.47
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry (2008) 1.45
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A (2007) 1.44
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc (2006) 1.43
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. J Mol Biol (2005) 1.40
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett (2007) 1.39
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Comput Biol (2006) 1.39
Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J Chem Phys (2005) 1.38
Why protein R-factors are so large: a self-consistent analysis. Proteins (2002) 1.36
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 1.36
Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys (2011) 1.34
Product-assisted catalysis in base-excision DNA repair. Nat Struct Biol (2003) 1.34
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys (2005) 1.33
One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers. J Phys Chem B (2006) 1.32
Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proc Natl Acad Sci U S A (2006) 1.32
pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. J Phys Chem B (2008) 1.32
Pi release from myosin: a simulation analysis of possible pathways. Structure (2010) 1.31
Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J Chem Phys (2004) 1.31
Application of elastic network models to proteins in the crystalline state. Biophys J (2009) 1.30
Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc (2002) 1.30
PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis. Proc Natl Acad Sci U S A (2010) 1.30
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins (2009) 1.29
Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. J Am Chem Soc (2003) 1.27
Carbon nanotube interaction with DNA. Nano Lett (2005) 1.27
Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. J Comput Chem (2001) 1.27
Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins (2005) 1.27
The origin of protein sidechain order parameter distributions. J Am Chem Soc (2004) 1.25
DNA polymorphism: a comparison of force fields for nucleic acids. Biophys J (2003) 1.25
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
A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proc Natl Acad Sci U S A (2003) 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
One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B (2008) 1.21
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
Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci U S A (2008) 1.19
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
Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations. Biophys J (2008) 1.18
The elastic properties of the structurally characterized myosin II S2 subdomain: a molecular dynamics and normal mode analysis. Biophys J (2008) 1.17
Importance of van der Waals Interactions in QM/MM Simulations. J Phys Chem B (2004) 1.16
A gating mechanism of pentameric ligand-gated ion channels. Proc Natl Acad Sci U S A (2013) 1.15
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
The signaling pathway of rhodopsin. Structure (2007) 1.11
Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations. J Chem Phys (2007) 1.11
Translocation mechanism of long sugar chains across the maltoporin membrane channel. Structure (2002) 1.11
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun (2013) 1.10
Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry. J Mol Biol (2005) 1.10
Dynamic distance disorder in proteins is caused by trapping. J Phys Chem B (2006) 1.10
Many local motions cooperate to produce the adenylate kinase conformational transition. J Mol Biol (2010) 1.10
Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase. Adv Protein Chem (2003) 1.10
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc (2006) 1.09
Hydrogen embrittlement of aluminum: the crucial role of vacancies. Phys Rev Lett (2005) 1.09
Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition. Biophys J (2002) 1.08
Interpreting correlated motions using normal mode analysis. Structure (2006) 1.08
Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. PLoS Comput Biol (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
Activation mechanism of a signaling protein at atomic resolution from advanced computations. J Am Chem Soc (2007) 1.06
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
Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations. Biophys J (2009) 1.05
Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. J Mol Biol (2002) 1.05
Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. J Phys Chem B (2006) 1.05
Native and non-native interactions along protein folding and unfolding pathways. Proteins (2002) 1.04
The unfolding action of GroEL on a protein substrate. Biophys J (2004) 1.04
Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues. J Am Chem Soc (2005) 1.04
Topological frustration in graphene nanoflakes: magnetic order and spin logic devices. Phys Rev Lett (2009) 1.04