Published in J Phys Chem B on April 06, 2006
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem (2008) 2.09
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B (2007) 1.59
QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase. J Chem Theory Comput (2007) 1.40
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9. J Phys Chem B (2007) 1.40
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys (2012) 1.39
Elucidation of the proton transport mechanism in human carbonic anhydrase II. J Am Chem Soc (2009) 1.37
pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. J Phys Chem B (2008) 1.32
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
Group theory and biomolecular conformation: I. Mathematical and computational models. J Phys Condens Matter (2010) 1.15
Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II. J Am Chem Soc (2011) 1.14
Preferred orientations of His64 in human carbonic anhydrase II. Biochemistry (2007) 1.13
"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
Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. J Mol Biol (2008) 1.07
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions. J Biol Inorg Chem (2009) 1.06
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
Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II. J Am Chem Soc (2008) 1.00
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
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
Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. Theochem (2009) 0.92
Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes. J Chem Theory Comput (2014) 0.91
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 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
Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys (2013) 0.89
QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway. J Am Chem Soc (2010) 0.89
Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study. Proteins (2011) 0.88
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
Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. J Chem Theory Comput (2014) 0.84
Proton transport in carbonic anhydrase: Insights from molecular simulation. Biochim Biophys Acta (2009) 0.84
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
Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci (2015) 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
Location of binding sites in small molecule rescue of human carbonic anhydrase II. Biophys J (2006) 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
Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions. J Chem Theory Comput (2008) 0.81
Investigation of the acetylation mechanism by GCN5 histone acetyltransferase. PLoS One (2012) 0.81
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B (2014) 0.80
Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase. J Comput Chem (2009) 0.79
Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase. J Mol Model (2011) 0.79
Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys (2016) 0.78
Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge. J Comput Aided Mol Des (2016) 0.78
DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput (2015) 0.78
Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors. J Med Chem (2013) 0.77
Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length. J Comput Aided Mol Des (2009) 0.77
QM/MM free energy simulations: recent progress and challenges. Mol Simul (2016) 0.76
Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase. J Phys Chem B (2013) 0.76
Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region. J Phys Chem B (2016) 0.75
pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis. J Phys Chem B (2011) 0.75
Computation of pH-dependent binding free energies. Biopolymers (2016) 0.75
Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem (2014) 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
Inhibitor and substrate binding by angiotensin-converting enzyme: quantum mechanical/molecular mechanical molecular dynamics studies. J Chem Inf Model (2011) 0.75
Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations. J Chem Phys (2015) 0.75
Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae. J Mol Model (2015) 0.75
Containing pandemic influenza with antiviral agents. Am J Epidemiol (2004) 12.82
Containing bioterrorist smallpox. Science (2002) 7.62
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol (2004) 7.38
Immune activation set point during early HIV infection predicts subsequent CD4+ T-cell changes independent of viral load. Blood (2004) 7.09
Combating trastuzumab resistance by targeting SRC, a common node downstream of multiple resistance pathways. Nat Med (2011) 6.21
Global gene expression profiling of multiple myeloma, monoclonal gammopathy of undetermined significance, and normal bone marrow plasma cells. Blood (2002) 5.47
A polymer tandem solar cell with 10.6% power conversion efficiency. Nat Commun (2013) 4.48
Do birth cohorts matter? Age-period-cohort analyses of the obesity epidemic in the United States. Soc Sci Med (2009) 3.87
Antiviral effects on influenza viral transmission and pathogenicity: observations from household-based trials. Am J Epidemiol (2006) 3.48
Hypoxia-dependent regulation of nonphagocytic NADPH oxidase subunit NOX4 in the pulmonary vasculature. Circ Res (2007) 3.28
Neuronal basis of age-related working memory decline. Nature (2011) 3.15
Internet-enabled interactive multimedia asthma education program: a randomized trial. Pediatrics (2003) 3.08
Two physically, functionally, and developmentally distinct peritoneal macrophage subsets. Proc Natl Acad Sci U S A (2010) 2.94
High-throughput solution processing of large-scale graphene. Nat Nanotechnol (2008) 2.93
Patterning organic single-crystal transistor arrays. Nature (2006) 2.80
The Na(V)1.7 sodium channel: from molecule to man. Nat Rev Neurosci (2012) 2.71
Conversion of channelrhodopsin into a light-gated chloride channel. Science (2014) 2.56
A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One (2011) 2.55
PTEN, PIK3CA, p-AKT, and p-p70S6K status: association with trastuzumab response and survival in patients with HER2-positive metastatic breast cancer. Am J Pathol (2010) 2.52
NMDA receptors subserve persistent neuronal firing during working memory in dorsolateral prefrontal cortex. Neuron (2013) 2.46
Reversal of autoimmunity by boosting memory-like autoregulatory T cells. Immunity (2010) 2.44
Cell-specific deletion of nitric oxide-sensitive guanylyl cyclase reveals a dual pathway for nitrergic neuromuscular transmission in the murine fundus. Gastroenterology (2013) 2.36
Nav1.8 expression is not restricted to nociceptors in mouse peripheral nervous system. Pain (2012) 2.34
Engaging in an auditory task suppresses responses in auditory cortex. Nat Neurosci (2009) 2.34
Exploratory analyses of efficacy data from major depressive disorder trials submitted to the US Food and Drug Administration in support of new drug applications. J Clin Psychiatry (2011) 2.33
Murine B7-H3 is a negative regulator of T cells. J Immunol (2004) 2.33
Planar heterojunction perovskite solar cells via vapor-assisted solution process. J Am Chem Soc (2013) 2.32
Containing a large bioterrorist smallpox attack: a computer simulation approach. Int J Infect Dis (2006) 2.29
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26
Protein 4.1R-dependent multiprotein complex: new insights into the structural organization of the red blood cell membrane. Proc Natl Acad Sci U S A (2008) 2.18
Association of the beta2-adrenergic receptor gene with essential hypertension in the non-Han Chinese Yi minority human population. J Hypertens (2006) 2.16
Hand, foot, and mouth disease in China: patterns of spread and transmissibility. Epidemiology (2011) 2.13
Protein structural variation in computational models and crystallographic data. Structure (2007) 2.13
14-3-3zeta Cooperates with ErbB2 to promote ductal carcinoma in situ progression to invasive breast cancer by inducing epithelial-mesenchymal transition. Cancer Cell (2009) 2.09
Human epithelial cancers secrete immunoglobulin g with unidentified specificity to promote growth and survival of tumor cells. Cancer Res (2003) 2.00
Stimulus-Dependent Neuronal Oscillations in Cat Visual Cortex: Inter-Columnar Interaction as Determined by Cross-Correlation Analysis. Eur J Neurosci (1990) 1.98
Mechanical Deformation Behavior of Nonpolar GaN Thick Films by Berkovich Nanoindentation. Nanoscale Res Lett (2009) 1.95
Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev (2013) 1.93
Texture signals in whisker vibrations. J Neurophysiol (2005) 1.93
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol (2004) 1.92
Expression of esophageal cancer related gene 4 (ECRG4), a novel tumor suppressor gene, in esophageal cancer and its inhibitory effect on the tumor growth in vitro and in vivo. Int J Cancer (2009) 1.92
Spectrins and ankyrinB constitute a specialized paranodal cytoskeleton. J Neurosci (2006) 1.90
Stimulus-Dependent Neuronal Oscillations in Cat Visual Cortex: Receptive Field Properties and Feature Dependence. Eur J Neurosci (1990) 1.86
Practical chemical sensors from chemically derived graphene. ACS Nano (2009) 1.85
A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure (2002) 1.84
Chemoimmunotherapy with low-dose fludarabine and cyclophosphamide and high dose rituximab in previously untreated patients with chronic lymphocytic leukemia. J Clin Oncol (2008) 1.84
A model of the ventral visual system based on temporal stability and local memory. PLoS Biol (2006) 1.83
Molecular imaging using labeled donor tissues reveals patterns of engraftment, rejection, and survival in transplantation. Transplantation (2005) 1.82
High heparanase activity in multiple myeloma is associated with elevated microvessel density. Cancer Res (2003) 1.81
Klf4 interacts directly with Oct4 and Sox2 to promote reprogramming. Stem Cells (2009) 1.79
Digital memory device based on tobacco mosaic virus conjugated with nanoparticles. Nat Nanotechnol (2006) 1.79
Heparan sulfate proteoglycans and heparanase--partners in osteolytic tumor growth and metastasis. Matrix Biol (2004) 1.75
Heparanase stimulation of protease expression implicates it as a master regulator of the aggressive tumor phenotype in myeloma. J Biol Chem (2008) 1.74
14-3-3zeta overexpression defines high risk for breast cancer recurrence and promotes cancer cell survival. Cancer Res (2009) 1.74
Dispersal state of multiwalled carbon nanotubes elicits profibrogenic cellular responses that correlate with fibrogenesis biomarkers and fibrosis in the murine lung. ACS Nano (2011) 1.74
Calcium phosphate nanoparticles with an asymmetric lipid bilayer coating for siRNA delivery to the tumor. J Control Release (2011) 1.72
TRPM5, a taste-signaling transient receptor potential ion-channel, is a ubiquitous signaling component in chemosensory cells. BMC Neurosci (2007) 1.69
Plasmonic polymer tandem solar cell. ACS Nano (2011) 1.68
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins (2006) 1.67
HSulf-1 and HSulf-2 are potent inhibitors of myeloma tumor growth in vivo. J Biol Chem (2005) 1.66
Polyaniline nanofiber/gold nanoparticle nonvolatile memory. Nano Lett (2005) 1.64
Enzymatic remodeling of heparan sulfate proteoglycans within the tumor microenvironment: growth regulation and the prospect of new cancer therapies. J Cell Biochem (2005) 1.64
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J (2006) 1.62
Antigen-specific B-1a antibodies induced by Francisella tularensis LPS provide long-term protection against F. tularensis LVS challenge. Proc Natl Acad Sci U S A (2009) 1.61
Intensification of Pacific storm track linked to Asian pollution. Proc Natl Acad Sci U S A (2007) 1.60
Inhibition of autophagy by 3-MA potentiates cisplatin-induced apoptosis in esophageal squamous cell carcinoma cells. Med Oncol (2009) 1.60
Safety and tolerability of sitagliptin in clinical studies: a pooled analysis of data from 10,246 patients with type 2 diabetes. BMC Endocr Disord (2010) 1.60
LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray. PLoS One (2012) 1.59
Umbilical myiasis in newborn. Indian Pediatr (2011) 1.57
Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc (2014) 1.56
Direct observation of colloidal aggregation by critical Casimir forces. Phys Rev Lett (2009) 1.55
mTOR complex component Rictor interacts with PKCzeta and regulates cancer cell metastasis. Cancer Res (2010) 1.54
Controllable self-induced passivation of hybrid lead iodide perovskites toward high performance solar cells. Nano Lett (2014) 1.54
A functional gamma-band defined by stimulus-dependent synchronization in area 18 of awake behaving cats. J Neurosci (2003) 1.53
Mitochondrial gene polymorphisms that protect mice from colitis. Gastroenterology (2013) 1.53
The presence of a membrane-bound progesterone receptor sensitizes the estradiol-induced effect on the proliferation of human breast cancer cells. Menopause (2011) 1.52
Low-temperature solution processing of graphene-carbon nanotube hybrid materials for high-performance transparent conductors. Nano Lett (2009) 1.50
Triggering of toll-like receptor-4 in human multiple myeloma cells promotes proliferation and alters cell responses to immune and chemotherapy drug attack. Cancer Biol Ther (2011) 1.50
Oncomodulin links inflammation to optic nerve regeneration. Proc Natl Acad Sci U S A (2009) 1.50
Long-term in vivo biodistribution imaging and toxicity of polyacrylic acid-coated upconversion nanophosphors. Biomaterials (2010) 1.50
Surgical management and evaluation of prognostic factors influencing postoperative visual outcome of suprasellar meningiomas. World Neurosurg (2011) 1.49
The guanine nucleotide exchange factor p63RhoGEF, a specific link between Gq/11-coupled receptor signaling and RhoA. J Biol Chem (2005) 1.49
Histone deacetylase inhibitor depsipeptide activates silenced genes through decreasing both CpG and H3K9 methylation on the promoter. Mol Cell Biol (2008) 1.48
Heparanase expression in gallbladder carcinoma and its correlation to prognosis. J Gastroenterol Hepatol (2007) 1.48
Evaluation of performance of some enrichment designs dealing with high placebo response in psychiatric clinical trials. Contemp Clin Trials (2011) 1.48
Dynamic Network Connectivity: A new form of neuroplasticity. Trends Cogn Sci (2010) 1.48
Kruppel-like factor 4 (Klf4) prevents embryonic stem (ES) cell differentiation by regulating Nanog gene expression. J Biol Chem (2010) 1.48
Surface charge and cellular processing of covalently functionalized multiwall carbon nanotubes determine pulmonary toxicity. ACS Nano (2013) 1.47
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem (2009) 1.46
Revealing atom-radical reactivity at low temperature through the N + OH reaction. Science (2011) 1.45
Autophagy negatively regulates cancer cell proliferation via selectively targeting VPRBP. Clin Sci (Lond) (2013) 1.45
Single-crystal linear polymers through visible light-triggered topochemical quantitative polymerization. Science (2014) 1.45
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry (2008) 1.45
Macrolide resistance and molecular types of Treponema pallidum causing primary syphilis in Shanghai, China. Clin Infect Dis (2009) 1.44
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