Published in J Phys Chem B on February 24, 2005
Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput Biol (2010) 1.76
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys (2008) 1.75
Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation. Biophys J (2007) 1.65
Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J (2005) 1.60
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Coarse-grained peptide modeling using a systematic multiscale approach. Biophys J (2007) 1.42
PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations. Biochemistry (2009) 1.40
Implicit solvent simulation models for biomembranes. Eur Biophys J (2005) 1.24
A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation. Chem Phys Lett (2014) 1.22
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J Chem Phys (2008) 1.20
Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B (2010) 1.19
Multiscale coarse-graining and structural correlations: connections to liquid-state theory. J Phys Chem B (2007) 1.18
Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles. J Chem Phys (2008) 1.15
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss (2010) 1.14
Systematic multiscale simulation of membrane protein systems. Curr Opin Struct Biol (2009) 1.12
Linear aggregation of proteins on the membrane as a prelude to membrane remodeling. Proc Natl Acad Sci U S A (2013) 1.09
A systematic methodology for defining coarse-grained sites in large biomolecules. Biophys J (2008) 1.09
Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. Biophys J (2013) 1.09
Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Biophys J (2012) 1.08
Solvent-free lipid bilayer model using multiscale coarse-graining. J Phys Chem B (2009) 1.05
Orientation of tie-lines in the phase diagram of DOPC/DPPC/cholesterol model biomembranes. Langmuir (2010) 1.04
Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys J (2008) 1.03
Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J (2008) 1.03
Hybrid coarse-graining approach for lipid bilayers at large length and time scales. J Phys Chem B (2009) 1.02
Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. J Chem Theory Comput (2006) 1.02
The power of coarse graining in biomolecular simulations. Wiley Interdiscip Rev Comput Mol Sci (2014) 1.00
Membrane binding and self-association of the epsin N-terminal homology domain. J Mol Biol (2012) 0.99
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One (2011) 0.98
A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations. J Phys Chem B (2010) 0.98
Multiscale simulation of microbe structure and dynamics. Prog Biophys Mol Biol (2011) 0.96
Modeling kinetics of subcellular disposition of chemicals. Chem Rev (2009) 0.96
An effective coarse-grained model for biological simulations: recent refinements and validations. Proteins (2014) 0.95
Systematic coarse-graining of a multicomponent lipid bilayer. J Phys Chem B (2009) 0.95
Multiscale characterization of protein conformational ensembles. Proteins (2009) 0.95
Multiscale coarse-graining of the protein energy landscape. PLoS Comput Biol (2010) 0.93
The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. J Chem Phys (2009) 0.93
Thermal nanostructure: an order parameter multiscale ensemble approach. J Chem Phys (2010) 0.93
Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1. Biophys J (2008) 0.93
Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. Biophys J (2009) 0.93
A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J Chem Theory Comput (2013) 0.92
Multiscale simulation of protein mediated membrane remodeling. Semin Cell Dev Biol (2009) 0.92
PRIMO: A Transferable Coarse-grained Force Field for Proteins. J Chem Theory Comput (2013) 0.91
Multiscale reactive molecular dynamics. J Chem Phys (2012) 0.91
Order parameters for macromolecules: application to multiscale simulation. J Chem Phys (2011) 0.90
Protein-mediated transformation of lipid vesicles into tubular networks. Biophys J (2013) 0.90
Time-resolved force distribution analysis. BMC Biophys (2013) 0.90
A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. J Chem Theory Comput (2009) 0.88
Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model (2013) 0.88
A coarse-grained model for amorphous and crystalline fatty acids. J Chem Phys (2010) 0.88
Multiscale simulations of heterogeneous model membranes. Biochim Biophys Acta (2008) 0.88
Reconstructing protein remodeled membranes in molecular detail from mesoscopic models. Phys Chem Chem Phys (2011) 0.87
Controlling cellular uptake of nanoparticles with pH-sensitive polymers. Sci Rep (2013) 0.87
Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion. J Chem Phys (2014) 0.86
Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation. PLoS One (2010) 0.86
Interactions between a voltage sensor and a toxin via multiscale simulations. Biophys J (2010) 0.86
Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys J (2005) 0.85
A structurally relevant coarse-grained model for cholesterol. Biophys J (2010) 0.85
Conformational temperature-dependent behavior of a histone H2AX: a coarse-grained Monte Carlo approach via knowledge-based interaction potentials. PLoS One (2012) 0.84
Membrane insertion of a voltage sensor helix. Biophys J (2011) 0.84
Microseconds dynamics simulations of the outer-membrane protease T. Biophys J (2007) 0.83
Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin. Biophys J (2010) 0.83
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins (2010) 0.83
Coarse-grained molecular dynamics simulations of phase transitions in mixed lipid systems containing LPA, DOPA, and DOPE lipids. Biophys J (2007) 0.81
Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model. J Chem Theory Comput (2015) 0.81
Molecular mechanics. Curr Pharm Des (2014) 0.81
Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations. Comput Biol Chem (2016) 0.81
Adaptive resolution simulations of biomolecular systems. Eur Biophys J (2017) 0.80
Recovering physical potentials from a model protein databank. Proc Natl Acad Sci U S A (2010) 0.80
Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.80
Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput (2014) 0.80
Point charges optimally placed to represent the multipole expansion of charge distributions. PLoS One (2013) 0.80
Hybrid coarse-grained/atomistic model of "chitosan + carbon nanostructures" composites. J Mol Model (2014) 0.79
A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent. J Chem Phys (2011) 0.79
Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering. J Chem Theory Comput (2014) 0.79
Combining optimal control theory and molecular dynamics for protein folding. PLoS One (2012) 0.79
Unified regression model of binding equilibria in crowded environments. Sci Rep (2011) 0.79
Peptide nanopores and lipid bilayers: interactions by coarse-grained molecular-dynamics simulations. Biophys J (2009) 0.79
Coarse-Grained Molecular Models of Water: A Review. Mol Simul (2012) 0.79
Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties. Adv Mater (2014) 0.79
Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model. J Chem Theory Comput (2014) 0.79
CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences. J Chem Phys (2015) 0.78
Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems. Int J Mol Sci (2010) 0.78
On-the-fly free energy parameterization via temperature accelerated molecular dynamics. Chem Phys Lett (2012) 0.78
Atomistic simulations of bicelle mixtures. Biophys J (2010) 0.78
Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers. Soft Matter (2012) 0.77
Design strategy of surface decoration for efficient delivery of nanoparticles by computer simulation. Sci Rep (2016) 0.77
Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. J Chem Theory Comput (2012) 0.77
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism. J Chem Phys (2015) 0.77
Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments. PLoS One (2012) 0.77
A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. Pac Symp Biocomput (2009) 0.77
Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput (2014) 0.77
Computational virology: From the inside out. Biochim Biophys Acta (2016) 0.76
Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach. J Chem Theory Comput (2013) 0.76
Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems. J Chem Theory Comput (2014) 0.76
Free-energy profiles of membrane insertion of the M2 transmembrane peptide from influenza A virus. Biophys J (2008) 0.76
Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. PLoS Comput Biol (2015) 0.76
Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration. J Chem Phys (2010) 0.76
Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. J Chem Theory Comput (2015) 0.76
Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.37
Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci U S A (2005) 1.97
Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophys J (2007) 1.96
Atomic crystal and molecular dynamics simulation structures of human carbonic anhydrase II: insights into the proton transfer mechanism. Biochemistry (2007) 1.83
Flexible simple point-charge water model with improved liquid-state properties. J Chem Phys (2006) 1.81
Structural basis of membrane bending by the N-BAR protein endophilin. Cell (2012) 1.80
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys (2008) 1.75
Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles. Biophys J (2002) 1.67
Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol (2007) 1.66
Multiscale coarse graining of liquid-state systems. J Chem Phys (2005) 1.65
Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation. Biophys J (2007) 1.65
A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium. J Chem Phys (2004) 1.63
Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J (2005) 1.60
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B (2007) 1.59
Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys J (2002) 1.56
Molecular dynamics simulation of proton transport through the influenza A virus M2 channel. Biophys J (2002) 1.55
Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations. Biophys J (2008) 1.53
The mechanism of proton exclusion in aquaporin channels. Proteins (2004) 1.49
Mechanism of membrane curvature sensing by amphipathic helix containing proteins. Biophys J (2011) 1.48
Coarse-graining methods for computational biology. Annu Rev Biophys (2013) 1.46
Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys J (2007) 1.45
Bridging microscopic and mesoscopic simulations of lipid bilayers. Biophys J (2002) 1.44
Coarse-grained peptide modeling using a systematic multiscale approach. Biophys J (2007) 1.42
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
Elucidation of the proton transport mechanism in human carbonic anhydrase II. J Am Chem Soc (2009) 1.37
The properties of ion-water clusters. I. The protonated 21-water cluster. J Chem Phys (2005) 1.34
Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway. Proc Natl Acad Sci U S A (2005) 1.34
Nucleotide-dependent conformational states of actin. Proc Natl Acad Sci U S A (2009) 1.33
Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation. Biophys J (2002) 1.31
Special pair dance and partner selection: elementary steps in proton transport in liquid water. J Phys Chem B (2008) 1.30
Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. J Phys Chem B (2006) 1.29
Actin filament remodeling by actin depolymerization factor/cofilin. Proc Natl Acad Sci U S A (2010) 1.28
New insights into BAR domain-induced membrane remodeling. Biophys J (2009) 1.27
Membrane binding by the endophilin N-BAR domain. Biophys J (2009) 1.24
Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys J (2008) 1.23
An improved multistate empirical valence bond model for aqueous proton solvation and transport. J Phys Chem B (2007) 1.22
A computational study of the closed and open states of the influenza a M2 proton channel. Biophys J (2005) 1.21
The curious case of the hydrated proton. Acc Chem Res (2011) 1.21
Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles. Biophys J (2005) 1.20
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J Chem Phys (2008) 1.20
A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor. Structure (2009) 1.19
Modeling real dynamics in the coarse-grained representation of condensed phase systems. J Chem Phys (2006) 1.19
Multiscale coarse-graining and structural correlations: connections to liquid-state theory. J Phys Chem B (2007) 1.18
Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. Biophys J (2006) 1.15
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss (2010) 1.14
Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II. J Am Chem Soc (2011) 1.14
Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster. J Am Chem Soc (2007) 1.14
Preferred orientations of His64 in human carbonic anhydrase II. Biochemistry (2007) 1.13
Systematic multiscale simulation of membrane protein systems. Curr Opin Struct Biol (2009) 1.12
A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. J Chem Phys (2005) 1.11
A computer simulation study of the hydrated proton in a synthetic proton channel. Biophys J (2003) 1.11
Multiscale simulation of transmembrane proteins. J Struct Biol (2006) 1.10
Gating of the mechanosensitive channel protein MscL: the interplay of membrane and protein. Biophys J (2008) 1.10
Linear aggregation of proteins on the membrane as a prelude to membrane remodeling. Proc Natl Acad Sci U S A (2013) 1.09
Proton transport pathway in the ClC Cl-/H+ antiporter. Biophys J (2009) 1.09
Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. Biophys J (2013) 1.09
A systematic methodology for defining coarse-grained sites in large biomolecules. Biophys J (2008) 1.09
Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophys J (2006) 1.08
Peptide folding using multiscale coarse-grained models. J Phys Chem B (2008) 1.06
Unique spatial heterogeneity in ionic liquids. J Am Chem Soc (2005) 1.06
Membrane docking geometry and target lipid stoichiometry of membrane-bound PKCα C2 domain: a combined molecular dynamics and experimental study. J Mol Biol (2010) 1.06
Multiscale coarse-graining of ionic liquids. J Phys Chem B (2006) 1.05
A multistate empirical valence bond description of protonatable amino acids. J Phys Chem A (2006) 1.05
Solvent-free lipid bilayer model using multiscale coarse-graining. J Phys Chem B (2009) 1.05
A bond-order analysis of the mechanism for hydrated proton mobility in liquid water. J Chem Phys (2005) 1.03
Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor. J Am Chem Soc (2013) 1.02
Hybrid coarse-graining approach for lipid bilayers at large length and time scales. J Phys Chem B (2009) 1.02
Enhancement of proton conductance by mutations of the selectivity filter of aquaporin-1. J Mol Biol (2011) 1.02
Insights into the mechanism of proton transport in cytochrome c oxidase. J Am Chem Soc (2012) 1.02
Protons may leak through pure lipid bilayers via a concerted mechanism. Biophys J (2005) 1.02
Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. J Chem Phys (2007) 1.02
Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials. J Phys Chem B (2008) 1.01
Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers. Biophys J (2004) 1.01
Properties of hydrated excess protons near phospholipid bilayers. J Phys Chem B (2010) 1.01
Structure and dynamics of the actin filament. J Mol Biol (2009) 1.01
Multiscale computer simulation of the immature HIV-1 virion. Biophys J (2010) 1.00
Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation. Biochim Biophys Acta (2007) 1.00
Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis. Biophys J (2008) 1.00
Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II. J Am Chem Soc (2008) 1.00
Intricate role of water in proton transport through cytochrome c oxidase. J Am Chem Soc (2010) 0.99
Membrane binding and self-association of the epsin N-terminal homology domain. J Mol Biol (2012) 0.99
Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models. Biophys J (2009) 0.99
Free energy profiles for H+ conduction in the D-pathway of Cytochrome c Oxidase: a study of the wild type and N98D mutant enzymes. Biochim Biophys Acta (2006) 0.98
Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations. J Chem Phys (2005) 0.98
Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules. Biophys J (2006) 0.98
Water under the BAR. Biophys J (2010) 0.97
Computational studies of proton transport through the M2 channel. FEBS Lett (2003) 0.96
A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics. J Chem Phys (2006) 0.96
Mechanisms of passive ion permeation through lipid bilayers: insights from simulations. J Phys Chem B (2006) 0.96
Multiscale coarse-graining of monosaccharides. J Phys Chem B (2007) 0.95
Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex. Biophys J (2008) 0.95
Systematic coarse-graining of a multicomponent lipid bilayer. J Phys Chem B (2009) 0.95
Molecular origins of cofilin-linked changes in actin filament mechanics. J Mol Biol (2013) 0.95
Ionic liquids. Acc Chem Res (2007) 0.94