Published in J Phys Chem B on February 15, 2008
Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. J Chem Theory Comput (2009) 1.23
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys (2009) 1.22
Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 1.14
Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach. SIAM J Appl Math (2011) 1.10
Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. J Chem Theory Comput (2011) 1.04
Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids. J Chem Phys (2010) 1.04
Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. Chem Phys Lett (2011) 0.97
Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force. Nonlinearity (2011) 0.96
Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput (2014) 0.92
Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation. J Chem Theory Comput (2013) 0.88
Dielectric pressure in continuum electrostatic solvation of biomolecules. Phys Chem Chem Phys (2012) 0.87
Electrostatic forces in the Poisson-Boltzmann systems. J Chem Phys (2013) 0.84
LS-VISM: A software package for analysis of biomolecular solvation. J Comput Chem (2015) 0.82
Motion of a Cylindrical Dielectric Boundary. SIAM J Appl Math (2013) 0.82
On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function. J Theor Comput Chem (2014) 0.82
Competitive adsorption and ordered packing of counterions near highly charged surfaces: From mean-field theory to Monte Carlo simulations. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.81
Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys (2008) 0.81
STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS. SIAM J Appl Math (2015) 0.79
Exploring accurate Poisson-Boltzmann methods for biomolecular simulations. Comput Theor Chem (2013) 0.79
Ionic Size Effects: Generalized Boltzmann Distributions, Counterion Stratification, and Modified Debye Length. Nonlinearity (2013) 0.79
Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates. Physica A (2010) 0.77
A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics. J Chem Phys (2015) 0.76
Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. J Phys Chem B (2016) 0.76
Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.76
DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT. SIAM J Appl Math (2015) 0.75
Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys (2016) 0.75
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem (2017) 0.75
MEAN-FIELD THEORY AND COMPUTATION OF ELECTROSTATICS WITH IONIC CONCENTRATION DEPENDENT DIELECTRICS. Commun Math Sci (2016) 0.75
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J (2004) 6.67
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet (2009) 6.42
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44
Glutamate receptor exocytosis and spine enlargement during chemically induced long-term potentiation. J Neurosci (2006) 3.84
Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH. Nature (2013) 3.22
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Whole-genome sequence of Schistosoma haematobium. Nat Genet (2012) 2.91
A critical role for beta cell M3 muscarinic acetylcholine receptors in regulating insulin release and blood glucose homeostasis in vivo. Cell Metab (2006) 2.82
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69
Altered ecosystem carbon and nitrogen cycles by plant invasion: a meta-analysis. New Phytol (2007) 2.68
Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58
Contribution of epithelial-derived fibroblasts to bleomycin-induced lung fibrosis. Am J Respir Crit Care Med (2009) 2.53
Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
IL-17-producing alveolar macrophages mediate allergic lung inflammation related to asthma. J Immunol (2008) 2.17
Ascaris suum draft genome. Nature (2011) 2.16
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Rosuvastatin alleviates diabetic cardiomyopathy by inhibiting NLRP3 inflammasome and MAPK pathways in a type 2 diabetes rat model. Cardiovasc Drugs Ther (2014) 2.16
Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A (2006) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10
Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09
A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06
Cancer cell-derived microvesicles induce transformation by transferring tissue transglutaminase and fibronectin to recipient cells. Proc Natl Acad Sci U S A (2011) 2.01
PAMAM nanoparticles promote acute lung injury by inducing autophagic cell death through the Akt-TSC2-mTOR signaling pathway. J Mol Cell Biol (2009) 2.00
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc (2004) 2.00
Enhancement of learning and memory by elevating brain magnesium. Neuron (2010) 2.00
Incoherent-light temporal stretching of high-speed intensity waveforms. Opt Lett (2014) 1.96
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys (2007) 1.93
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
CH4 and N2O emissions from Spartina alterniflora and Phragmites australis in experimental mesocosms. Chemosphere (2007) 1.91
Experience-dependent modification of a central amygdala fear circuit. Nat Neurosci (2013) 1.88
A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci U S A (2010) 1.87
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol (2011) 1.86
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem (2004) 1.81
Responses of ecosystem carbon cycle to experimental warming: a meta-analysis. Ecology (2013) 1.80
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80
Increased and prolonged pulmonary fibrosis in surfactant protein C-deficient mice following intratracheal bleomycin. Am J Pathol (2005) 1.76
Competition between phasic and asynchronous release for recovered synaptic vesicles at developing hippocampal autaptic synapses. J Neurosci (2004) 1.76
POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model (2010) 1.75
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (2008) 1.75
Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights. PLoS Biol (2010) 1.74
Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys (2007) 1.73
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
ATF4 regulates MYC-mediated neuroblastoma cell death upon glutamine deprivation. Cancer Cell (2012) 1.71
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69
Human pregnancy up-regulates Tim-3 in innate immune cells for systemic immunity. J Immunol (2009) 1.68
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67
A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2005) 1.66
Multiple residues in the second extracellular loop are critical for M3 muscarinic acetylcholine receptor activation. J Biol Chem (2007) 1.65
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Optimal vaccination strategies for 2009 pandemic H1N1 and seasonal influenza vaccines in humans. Vaccine (2010) 1.65
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65
Regulation of HIF-1alpha and VEGF by miR-20b tunes tumor cells to adapt to the alteration of oxygen concentration. PLoS One (2009) 1.65
Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol (2005) 1.64
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model (2008) 1.64
Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc (2002) 1.63
SCF-mediated mast cell infiltration and activation exacerbate the inflammation and immunosuppression in tumor microenvironment. Blood (2008) 1.63
Targeted immunomodulation of the NF-kappaB pathway in airway epithelium impacts host defense against Pseudomonas aeruginosa. J Immunol (2006) 1.62
Simvastatin-mediated upregulation of VEGF and BDNF, activation of the PI3K/Akt pathway, and increase of neurogenesis are associated with therapeutic improvement after traumatic brain injury. J Neurotrauma (2008) 1.62
Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci U S A (2012) 1.62
Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62
Immediate autotransplantation of mandibular third molar in China. Oral Surg Oral Med Oral Pathol Oral Radiol Endod (2010) 1.60
Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput (2008) 1.52
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc (2005) 1.51
Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol (2008) 1.51
Ecosystem carbon stock influenced by plantation practice: implications for planting forests as a measure of climate change mitigation. PLoS One (2010) 1.51
Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol (2014) 1.46
How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput (2010) 1.44
Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov (2011) 1.44
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys (2007) 1.43
The physical basis of microtubule structure and stability. Protein Sci (2003) 1.43
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J (2006) 1.42
Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41
Small-for-size syndrome after living donor liver transplantation: successful treatment with a transjugular intrahepatic portosystemic shunt. Liver Transpl (2012) 1.41
Prophylaxis against hepatitis B virus recurrence after liver transplantation for hepatitis B virus-related end-stage liver diseases with severe hypersplenism and splenomegaly: role of splenectomy. J Surg Res (2012) 1.41
Effects of temperature on the development and population growth of the sycamore lace bug, Corythucha ciliata. J Insect Sci (2011) 1.41
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38
The significance of degenerate processes to enantioselective olefin metathesis reactions promoted by stereogenic-at-Mo complexes. J Am Chem Soc (2009) 1.37
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res (2006) 1.37
The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc (2006) 1.37
p47phox deficiency impairs NF-kappa B activation and host defense in Pseudomonas pneumonia. J Immunol (2004) 1.36
Responses of ecosystem nitrogen cycle to nitrogen addition: a meta-analysis. New Phytol (2010) 1.36
The Rho-linked mental retardation protein oligophrenin-1 controls synapse maturation and plasticity by stabilizing AMPA receptors. Genes Dev (2009) 1.35