Published in Biophys J on June 22, 2011
On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. J Chem Phys (2013) 1.20
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J (2012) 1.15
Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy. J Phys Chem B (2013) 1.04
Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. J Phys Chem B (2013) 1.04
NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophys J (2013) 1.01
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J (2011) 0.98
Combining experiments and simulations using the maximum entropy principle. PLoS Comput Biol (2014) 0.92
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput (2013) 0.90
Comparative analysis of the orientation of transmembrane peptides using solid-state (2)H- and (15)N-NMR: mobility matters. Eur Biophys J (2012) 0.83
Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophys J (2015) 0.79
Structural determination of virus protein U from HIV-1 by NMR in membrane environments. Biochim Biophys Acta (2015) 0.77
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol (2015) 0.77
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct (1999) 10.13
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem (2008) 5.81
Simultaneous determination of protein structure and dynamics. Nature (2005) 5.28
Generalized born model with a simple smoothing function. J Comput Chem (2003) 4.36
Imaging membrane protein helical wheels. J Magn Reson (2000) 3.80
A solid-state NMR index of helical membrane protein structure and topology. J Magn Reson (2000) 3.67
Helical membrane protein folding, stability, and evolution. Annu Rev Biochem (2000) 3.63
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B (2005) 3.32
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One (2007) 2.65
Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys J (2006) 2.30
Ensemble refinement of protein crystal structures: validation and application. Structure (2007) 2.16
Tilt angles of transmembrane model peptides in oriented and non-oriented lipid bilayers as determined by 2H solid-state NMR. Biophys J (2004) 1.98
Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes. J R Soc Interface (2009) 1.77
Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. J Mol Biol (2005) 1.76
High-resolution NMR spectroscopy of membrane proteins in aligned bicelles. J Am Chem Soc (2004) 1.76
Convergence of molecular dynamics simulations of membrane proteins. Proteins (2007) 1.75
Solid-state NMR investigation of the membrane-disrupting mechanism of antimicrobial peptides MSI-78 and MSI-594 derived from magainin 2 and melittin. Biophys J (2006) 1.70
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci U S A (2005) 1.66
On the orientation of a designed transmembrane peptide: toward the right tilt angle? J Am Chem Soc (2007) 1.54
Structural dynamics and topology of phospholamban in oriented lipid bilayers using multidimensional solid-state NMR. Biochemistry (2006) 1.53
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem (2005) 1.48
Orientation and dynamics of peptides in membranes calculated from 2H-NMR data. Biophys J (2009) 1.43
A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose. Biophys J (2005) 1.42
Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science (1993) 1.40
Transmembrane helix tilting: insights from calculating the potential of mean force. Phys Rev Lett (2008) 1.35
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophys J (2010) 1.31
Rotational diffusion of membrane proteins in aligned phospholipid bilayers by solid-state NMR spectroscopy. J Magn Reson (2005) 1.29
Structure, dynamics, and assembly of filamentous bacteriophages by nuclear magnetic resonance spectroscopy. Annu Rev Phys Chem (2008) 1.22
Orientation and dynamics of transmembrane peptides: the power of simple models. Eur Biophys J (2009) 1.18
Conformational variability of solution nuclear magnetic resonance structures. J Mol Biol (1995) 1.06
Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J Phys Chem B (2005) 1.04
Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson (2008) 1.03
Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide. Biophys J (2010) 1.02
Assessing the effects of time and spatial averaging in 15N chemical shift/15N-1H dipolar correlation solid state NMR experiments. J Biomol NMR (2003) 1.00
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J (2011) 0.98
Influence of whole-body dynamics on 15N PISEMA NMR spectra of membrane proteins: a theoretical analysis. Biophys J (2009) 0.98
Implementation and application of helix-helix distance and crossing angle restraint potentials. J Comput Chem (2007) 0.95
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. J Comput Chem (2010) 0.88
CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem (2008) 5.81
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One (2007) 2.65
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Theoretical and computational models of biological ion channels. Q Rev Biophys (2004) 2.41
Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys (2004) 2.00
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys J (2004) 1.91
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem (2014) 1.89
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH. J Mol Biol (2007) 1.53
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem (2005) 1.48
Transmembrane helix tilting: insights from calculating the potential of mean force. Phys Rev Lett (2008) 1.35
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophys J (2010) 1.31
Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. J Am Chem Soc (2011) 1.29
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J (2012) 1.15
Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc (2004) 1.14
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR (2005) 1.12
Molecular dynamics studies of ion permeation in VDAC. Biophys J (2011) 1.09
Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages. Mol Biol Cell (2011) 1.09
Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B (2010) 1.07
Generation and application of new rat monoclonal antibodies against synthetic FLAG and OLLAS tags for improved immunodetection. J Immunol Methods (2007) 1.05
Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson (2008) 1.03
Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association. J Am Chem Soc (2008) 1.03
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem (2011) 1.02
NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophys J (2013) 1.01
Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophys J (2013) 1.01
Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. Biophys J (2011) 1.00
CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. J Chem Inf Model (2013) 0.99
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J (2011) 0.98
Transmembrane helix assembly by window exchange umbrella sampling. Phys Rev Lett (2012) 0.97
NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. Biophys J (2012) 0.97
Improving the CHARMM force field for polyunsaturated fatty acid chains. J Phys Chem B (2012) 0.96
Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res (2012) 0.96
Implementation and application of helix-helix distance and crossing angle restraint potentials. J Comput Chem (2007) 0.95
Brownian dynamics simulations of ion transport through the VDAC. Biophys J (2011) 0.94
Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study. Proteins (2006) 0.94
Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa. J Am Chem Soc (2010) 0.93
Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J Comput Chem (2011) 0.92
Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys J (2002) 0.89
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol (2013) 0.89
Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers. Biophys J (2009) 0.88
Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly. J Chem Theory Comput (2012) 0.88
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. J Comput Chem (2010) 0.88
Identification of ligand templates using local structure alignment for structure-based drug design. J Chem Inf Model (2012) 0.87
A repulsive electrostatic mechanism for protein export through the type III secretion apparatus. Biophys J (2010) 0.87
ST-analyzer: a web-based user interface for simulation trajectory analysis. J Comput Chem (2014) 0.86
Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. J Phys Chem B (2014) 0.86
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. J Chem Inf Model (2012) 0.86
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. J Comput Chem (2009) 0.86
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. J Comput Chem (2013) 0.85
Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating. Biophys J (2011) 0.85
Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes. Proteins (2009) 0.85
CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. J Chem Inf Model (2014) 0.84
How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? J Chem Theory Comput (2015) 0.84
Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. J Phys Chem B (2011) 0.83
Protein dynamics and ion traffic in bacterioferritin. Biochemistry (2012) 0.82
Design, solid-phase synthesis, and evaluation of a phenyl-piperazine-triazine scaffold as α-helix mimetics. ACS Comb Sci (2014) 0.82
Assessing smectic liquid-crystal continuum models for elastic bilayer deformations. Chem Phys Lipids (2013) 0.82
Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry (2015) 0.81
Lipopolysaccharide membrane building and simulation. Methods Mol Biol (2015) 0.80
A novel strategy to determine protein structures using exclusively residual dipolar coupling. J Comput Chem (2008) 0.80
Quantification of Drive-Response Relationships Between Residues During Protein Folding. J Chem Theory Comput (2013) 0.80
Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors. J Chem Inf Model (2012) 0.78
Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. J Comput Chem (2007) 0.77
Ligand binding site detection by local structure alignment and its performance complementarity. J Chem Inf Model (2013) 0.77
Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein. Biochemistry (2016) 0.76
Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol (2015) 0.75
Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation Between Binary Bilayers. J Chem Theory Comput (2019) 0.75
Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. J Phys Chem B (2016) 0.75
Transmembrane Motions of PglB Induced by LLO are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity. Glycobiology (2017) 0.75
NMR characterization of hydrophobic collapses in amyloidogenic unfolded states and their implications for amyloid formation. Biochem Biophys Res Commun (2010) 0.75