Published in Proc Natl Acad Sci U S A on December 08, 2008
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Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A (2007) 1.27
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Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry (2004) 1.22
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Identification of a functionally impaired positive regulatory domain I binding factor 1 transcription repressor in myeloma cell lines. J Immunol (2003) 1.22
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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
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Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations. Biophys J (2008) 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
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Many local motions cooperate to produce the adenylate kinase conformational transition. J Mol Biol (2010) 1.10
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Interpreting correlated motions using normal mode analysis. Structure (2006) 1.08
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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
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
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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
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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
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
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
A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability. Biophys J (2009) 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
Growth differentiating factor 15 enhances the tumor-initiating and self-renewal potential of multiple myeloma cells. Blood (2013) 0.95
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
Automatized parametrization of SCC-DFTB repulsive potentials: application to hydrocarbons. J Phys Chem A (2009) 0.93
Two-photon fluorescence and second-harmonic generation imaging of collagen in human tissue based on multiphoton microscopy. Scanning (2011) 0.93
Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering. Biophys J (2010) 0.92
Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. J Am Chem Soc (2002) 0.92
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
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
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
What governs the charge transfer in DNA? The role of DNA conformation and environment. J Phys Chem B (2008) 0.91
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discuss (2013) 0.90
Regulation and specificity of MHC2TA promoter usage in human primary T lymphocytes and cell line. J Immunol (2002) 0.90
Transmembrane peptides used to investigate the homo-oligomeric interface and binding hotspot of latent membrane protein 1. Biopolymers (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
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