Published in J Phys Chem B on October 28, 2010
Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Biophys J (2012) 1.08
Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. PLoS Comput Biol (2013) 1.00
Molecular design, structures, and activity of antimicrobial peptide-mimetic polymers. Macromol Biosci (2013) 0.90
Bacterial membrane activity of α-peptide/β-peptoid chimeras: influence of amino acid composition and chain length on the activity against different bacterial strains. BMC Microbiol (2011) 0.87
Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3. Biophys J (2014) 0.87
Atomic-level description of protein-lipid interactions using an accelerated membrane model. Biochim Biophys Acta (2016) 0.81
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05
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
SCN5A mutations associate with arrhythmic dilated cardiomyopathy and commonly localize to the voltage-sensing mechanism. J Am Coll Cardiol (2011) 1.95
Primate-specific microRNA-637 inhibits tumorigenesis in hepatocellular carcinoma by disrupting signal transducer and activator of transcription 3 signaling. Hepatology (2011) 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
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
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Molecular dynamics simulations of a fluid near its critical point. Phys Rev Lett (2004) 1.39
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Comput Biol (2006) 1.39
Thymopoietin (lamina-associated polypeptide 2) gene mutation associated with dilated cardiomyopathy. Hum Mutat (2005) 1.37
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 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
Prevalence of desmin mutations in dilated cardiomyopathy. Circulation (2007) 1.28
Entropy-based mechanism of ribosome-nucleoid segregation in E. coli cells. Biophys J (2011) 1.24
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.24
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
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
Effect of macromolecular crowding on reaction rates: a computational and theoretical study. Biophys J (2009) 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
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
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
MicroRNA-204 regulates vascular smooth muscle cell calcification in vitro and in vivo. Cardiovasc Res (2012) 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
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
Role of CBP and SATB-1 in aging, dietary restriction, and insulin-like signaling. PLoS Biol (2009) 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
An aligned nanofibrous collagen scaffold by electrospinning and its effects on in vitro fibroblast culture. J Biomed Mater Res A (2006) 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
Mesenchymal stem cells modified with miR-126 release angiogenic factors and activate Notch ligand Delta-like-4, enhancing ischemic angiogenesis and cell survival. Int J Mol Med (2012) 1.04
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
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
Transcriptional and epigenetic regulation of human microRNAs. Cancer Lett (2012) 1.02
MYC protein inhibits transcription of the microRNA cluster MC-let-7a-1~let-7d via noncanonical E-box. J Biol Chem (2011) 1.02
Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework. Biophys J (2008) 1.01
Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol (2013) 1.01
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
Formation of collagen-glycosaminoglycan blended nanofibrous scaffolds and their biological properties. Biomacromolecules (2005) 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
Danon disease presenting with dilated cardiomyopathy and a complex phenotype. J Hum Genet (2007) 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
Sulforaphane induces cell cycle arrest and apoptosis in acute lymphoblastic leukemia cells. PLoS One (2012) 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
A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability. Biophys J (2009) 0.96
Periostin contributes to the acquisition of multipotent stem cell-like properties in human mammary epithelial cells and breast cancer cells. PLoS One (2013) 0.96
Microfluidic based platform for characterization of protein interactions in hydrogel nanoenvironments. Anal Chem (2007) 0.95
Lateral diffusion and percolation in membranes. Phys Rev Lett (2006) 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
Ursolic acid promotes cancer cell death by inducing Atg5-dependent autophagy. Int J Cancer (2013) 0.93
The development of a serum-free derived bioengineered conjunctival epithelial equivalent using an ultrathin poly(epsilon-caprolactone) membrane substrate. Invest Ophthalmol Vis Sci (2006) 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
A multi-pass pumping scheme for thin disk lasers with good anti-disturbance ability. Opt Express (2015) 0.91
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
Crowding effects on association reactions at membranes. Biophys J (2010) 0.91
Apelin-APJ induces ICAM-1, VCAM-1 and MCP-1 expression via NF-κB/JNK signal pathway in human umbilical vein endothelial cells. Amino Acids (2012) 0.91
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Ghrelin attenuates the osteoblastic differentiation of vascular smooth muscle cells through the ERK pathway. PLoS One (2012) 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
Lateral diffusion of proteins in the plasma membrane: spatial tessellation and percolation theory. J Phys Chem B (2007) 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
Identification of the Ah-receptor structural determinants for ligand preferences. Toxicol Sci (2012) 0.89
Three-dimensional microchannels in biodegradable polymeric films for control orientation and phenotype of vascular smooth muscle cells. Tissue Eng (2006) 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
Effects of temperature and salt concentration on the structural stability of human lymphotactin: insights from molecular simulations. J Am Chem Soc (2006) 0.88
Preferential interactions between small solutes and the protein backbone: a computational analysis. Biochemistry (2010) 0.87
Anisotropic diffusion of elongated and aligned polymer chains in a nematic solvent. J Phys Chem B (2006) 0.87
Characterization of nanofibers formed by self-assembly of beta-peptide oligomers using small angle x-ray scattering. J Chem Phys (2008) 0.86
Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase. Biophys J (2011) 0.86
Apoptosis induced by 1,3,6,7-tetrahydroxyxanthone in Hepatocellular carcinoma and proteomic analysis. Apoptosis (2012) 0.85
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
The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding. J Chem Phys (2007) 0.85