Published in J Phys Chem B on March 02, 2006
Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques. PLoS Comput Biol (2011) 1.12
Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics. Biochemistry (2009) 1.03
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry (2013) 0.96
Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study. Nucleic Acids Res (2012) 0.95
An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization. J Chem Phys (2013) 0.94
Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer's disease. J Mol Biol (2011) 0.93
Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations. J Chem Phys (2008) 0.87
Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories. J Chem Theory Comput (2014) 0.87
Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor. J Phys Chem B (2009) 0.85
Autoinhibition of endophilin in solution via interdomain interactions. Biophys J (2013) 0.85
Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des (2011) 0.83
Metadynamics studies of crystal nucleation. IUCrJ (2015) 0.82
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. J Chem Theory Comput (2015) 0.82
Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism. Biophys J (2013) 0.82
Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase. Sci Rep (2016) 0.81
Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin. Proc Natl Acad Sci U S A (2016) 0.80
MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone. J Mol Biol (2016) 0.78
Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. J Chem Theory Comput (2014) 0.78
The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics. Methods Mol Biol (2015) 0.78
Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem (2015) 0.78
Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability. J Med Chem (2016) 0.78
Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations. J Mol Graph Model (2016) 0.78
Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes. J Mol Model (2008) 0.77
Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics. Sci Rep (2016) 0.76
Ion conduction through the hERG potassium channel. PLoS One (2012) 0.76
Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example. Biophys J (2016) 0.76
Molecular Basis of Filtering Carbapenems by Porins from β-Lactam-resistant Clinical Strains of Escherichia coli. J Biol Chem (2015) 0.76
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proc Natl Acad Sci U S A (2017) 0.75
Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. Adv Exp Med Biol (2014) 0.75
A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity. PLoS One (2014) 0.75
Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors. ACS Chem Biol (2016) 0.75
Effects of FGFR2 kinase activation loop dynamics on catalytic activity. PLoS Comput Biol (2017) 0.75
A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions. Sci Rep (2016) 0.75
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (2017) 0.75
DNA mutation motifs in the genes associated with inherited diseases. PLoS One (2017) 0.75
Prion protein β2-α2 loop conformational landscape. Proc Natl Acad Sci U S A (2017) 0.75
H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes. Biophys J (2017) 0.75
Canonical sampling through velocity rescaling. J Chem Phys (2007) 12.40
Escaping free-energy minima. Proc Natl Acad Sci U S A (2002) 7.98
Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys Rev Lett (2008) 3.06
From A to B in free energy space. J Chem Phys (2007) 1.74
A bias-exchange approach to protein folding. J Phys Chem B (2007) 1.72
Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc (2006) 1.56
The nature and transport mechanism of hydrated hydroxide ions in aqueous solution. Nature (2002) 1.55
Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett (2006) 1.54
Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys Rev Lett (2003) 1.54
Assessing the accuracy of metadynamics. J Phys Chem B (2005) 1.54
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations. PLoS Comput Biol (2009) 1.46
Flexible docking in solution using metadynamics. J Am Chem Soc (2005) 1.43
Entropy-driven genome organization. Biophys J (2006) 1.42
On the recombination of hydronium and hydroxide ions in water. Proc Natl Acad Sci U S A (2011) 1.42
Stacking and T-shape competition in aromatic-aromatic amino acid interactions. J Am Chem Soc (2002) 1.40
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J Chem Phys (2004) 1.37
The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc Chem Res (2002) 1.37
Nucleotide-dependent conformational states of actin. Proc Natl Acad Sci U S A (2009) 1.33
Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations. J Am Chem Soc (2009) 1.32
Nucleation mechanism for the direct graphite-to-diamond phase transition. Nat Mater (2011) 1.29
DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting. Proc Natl Acad Sci U S A (2009) 1.24
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J Mol Biol (2002) 1.22
Generalized neural-network representation of high-dimensional potential-energy surfaces. Phys Rev Lett (2007) 1.20
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proc Natl Acad Sci U S A (2013) 1.18
Hydrogen bonding in water. Phys Rev Lett (2003) 1.17
Funnel metadynamics as accurate binding free-energy method. Proc Natl Acad Sci U S A (2013) 1.17
The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin. J Am Chem Soc (2008) 1.16
Targeting biomolecular flexibility with metadynamics. Curr Opin Struct Biol (2010) 1.16
Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness. J Mol Biol (2003) 1.13
Conformational changes and gating at the selectivity filter of potassium channels. J Am Chem Soc (2008) 1.13
Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics. Biophys J (2008) 1.13
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proc Natl Acad Sci U S A (2010) 1.12
Geometry and physics of proteins. Proteins (2002) 1.12
Crystal structure transformations in SiO2 from classical and ab initio metadynamics. Nat Mater (2006) 1.12
Signature of tetrahedral Ge in the Raman spectrum of amorphous phase-change materials. Phys Rev Lett (2010) 1.11
Nonperiodic boundary conditions for solvated systems. J Chem Phys (2005) 1.11
A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. J Phys Chem B (2005) 1.09
A molecular spring for vision. J Am Chem Soc (2004) 1.09
Proton transfer through the water gossamer. Proc Natl Acad Sci U S A (2013) 1.08
Knotted vs. unknotted proteins: evidence of knot-promoting loops. PLoS Comput Biol (2010) 1.07
Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophys J (2006) 1.07
Exploring the gating mechanism in the ClC chloride channel via metadynamics. J Mol Biol (2006) 1.06
Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics. Phys Rev Lett (2007) 1.05
A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion. J Am Chem Soc (2004) 1.04
Reconstructing the density of states by history-dependent metadynamics. Phys Rev Lett (2004) 1.04
Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants. J Mol Biol (2007) 1.04
Asprich peptides are occluded in calcite and permanently disorder biomineral crystals. J Am Chem Soc (2010) 1.04
Sampling protein motion and solvent effect during ligand binding. Proc Natl Acad Sci U S A (2012) 1.04
The G-triplex DNA. Angew Chem Int Ed Engl (2013) 1.04
Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. J Am Chem Soc (2005) 1.03
Exploring complex protein-ligand recognition mechanisms with coarse metadynamics. J Phys Chem B (2009) 1.03
Anisotropy of Earth's D'' layer and stacking faults in the MgSiO3 post-perovskite phase. Nature (2005) 1.03
Microscopic Mechanism of Antibiotics Translocation through a Porin. Biophys J (2004) 1.03
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc (2009) 1.02
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling. J Chem Phys (2009) 1.01
Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations. PLoS Comput Biol (2012) 1.01
From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci U S A (2011) 1.01
Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties. Cancer Cell (2013) 1.01
A time-independent free energy estimator for metadynamics. J Phys Chem B (2014) 1.01
The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases. J Am Chem Soc (2007) 1.00
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Protein Sci (2008) 0.99
Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. Proc Natl Acad Sci U S A (2013) 0.99
Influence of DNA structure on the reactivity of the guanine radical cation. Chemistry (2004) 0.98
Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding. J Am Chem Soc (2006) 0.98
Using sketch-map coordinates to analyze and bias molecular dynamics simulations. Proc Natl Acad Sci U S A (2012) 0.98
Dispersion corrections to density functionals for water aromatic interactions. J Chem Phys (2004) 0.97
Convergent dynamics in the protease enzymatic superfamily. J Am Chem Soc (2006) 0.97
A molecular dynamics study of the early stages of calcium carbonate growth. J Phys Chem B (2009) 0.97
Accurate sampling using Langevin dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.96
A self-learning algorithm for biased molecular dynamics. Proc Natl Acad Sci U S A (2010) 0.95
Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations. J Am Chem Soc (2011) 0.95
The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J Chem Phys (2005) 0.94
Inferring the diameter of a biopolymer from its stretching response. Biophys J (2005) 0.94
Force generation in lamellipodia is a probabilistic process with fast growth and retraction events. Biophys J (2010) 0.94
Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism. J Am Chem Soc (2011) 0.94
The allosteric communication pathways in KIX domain of CBP. Proc Natl Acad Sci U S A (2013) 0.93
Advillin folding takes place on a hypersurface of small dimensionality. Phys Rev Lett (2008) 0.92
Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19. PLoS Comput Biol (2013) 0.92
Essential dynamics of helices provide a functional classification of EF-hand proteins. J Proteome Res (2007) 0.91
Freezing of a Lennard-Jones fluid: from nucleation to spinodal regime. Phys Rev Lett (2006) 0.91
Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell (2013) 0.91
Exploring the universe of protein structures beyond the Protein Data Bank. PLoS Comput Biol (2010) 0.91