Published in Proc Natl Acad Sci U S A on April 04, 2005
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Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. J Chem Theory Comput (2012) 0.90
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The influence of 1-alkanols and external pressure on the lateral pressure profiles of lipid bilayers. Biophys J (2008) 0.83
Structure of the DMPC lipid bilayer ripple phase. Soft Matter (2015) 0.82
Ripple formation in unilamellar-supported lipid bilayer revealed by FRAPP. Eur Phys J E Soft Matter (2013) 0.79
Effects of palmitoylation on dynamics and phospholipid-bilayer-perturbing properties of the N-terminal segment of pulmonary surfactant protein SP-C as shown by 2H-NMR. Biophys J (2008) 0.79
Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations. J Chem Phys (2011) 0.79
Dynamics of the gel to fluid phase transformation in unilamellar DPPC vesicles. J Phys Chem B (2012) 0.77
The thermodynamics of simple biomembrane mimetic systems. J Pharm Bioallied Sci (2011) 0.75
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New ordered metastable phases between the gel and subgel phases in hydrated phospholipids. Biophys J (2001) 0.94
Structure of the ripple phase of phospholipid multibilayers. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.88
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B (2007) 9.56
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem (2004) 8.13
Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J (2011) 2.43
The molecular face of lipid rafts in model membranes. Proc Natl Acad Sci U S A (2008) 2.24
Antimicrobial peptides in action. J Am Chem Soc (2006) 2.09
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. J Am Chem Soc (2003) 2.00
The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J Am Chem Soc (2003) 1.83
Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput Biol (2010) 1.76
The Role of histidine residues in low-pH-mediated viral membrane fusion. Structure (2006) 1.75
Toroidal pores formed by antimicrobial peptides show significant disorder. Biochim Biophys Acta (2008) 1.73
Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci (2004) 1.66
Molecular dynamics simulations of hydrophilic pores in lipid bilayers. Biophys J (2004) 1.65
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein. J Am Chem Soc (2004) 1.65
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc Natl Acad Sci U S A (2002) 1.64
Basic ingredients of free energy calculations: a review. J Comput Chem (2010) 1.60
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem Phys Lipids (2005) 1.56
Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J Am Chem Soc (2003) 1.56
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc Natl Acad Sci U S A (2011) 1.50
A new force field for simulating phosphatidylcholine bilayers. J Comput Chem (2010) 1.43
Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem Biol (2014) 1.39
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J Comput Chem (2002) 1.36
Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. J Am Chem Soc (2009) 1.33
Simulation of MscL gating in a bilayer under stress. Biophys J (2003) 1.31
3D pressure field in lipid membranes and membrane-protein complexes. Phys Rev Lett (2009) 1.30
Release of content through mechano-sensitive gates in pressurized liposomes. Proc Natl Acad Sci U S A (2010) 1.26
The molecular mechanism of lipid monolayer collapse. Proc Natl Acad Sci U S A (2008) 1.26
Mechanosensitive membrane channels in action. Biophys J (2008) 1.25
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study. Biochim Biophys Acta (2006) 1.21
Molecular view of hexagonal phase formation in phospholipid membranes. Biophys J (2004) 1.21
Lipid organization of the plasma membrane. J Am Chem Soc (2014) 1.20
Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. J Am Chem Soc (2012) 1.20
Histidine protonation and the activation of viral fusion proteins. Biochem Soc Trans (2008) 1.15
Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophys J (2009) 1.14
Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Phys Chem Chem Phys (2009) 1.14
Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin. Proteins (2002) 1.13
Transmembrane helices can induce domain formation in crowded model membranes. Biochim Biophys Acta (2011) 1.12
Partitioning of lipids at domain boundaries in model membranes. Biophys J (2010) 1.10
Reconstruction of atomistic details from coarse-grained structures. J Comput Chem (2010) 1.10
Molecular simulation as an aid to experimentalists. Curr Opin Struct Biol (2008) 1.09
Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. Faraday Discuss (2010) 1.09
Ion transport across transmembrane pores. Biophys J (2007) 1.09
Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A (2005) 1.08
Molecular mechanism of cyclodextrin mediated cholesterol extraction. PLoS Comput Biol (2011) 1.08
Monolayer ice. Phys Rev Lett (2003) 1.07
Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. J Am Chem Soc (2004) 1.06
Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Phys Chem Chem Phys (2010) 1.05
A dynamic pharmacophore drives the interaction between Psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a. Mol Pharmacol (2011) 1.05
Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Sci Rep (2013) 1.05
Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys Chem Chem Phys (2011) 1.04
Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. J Am Chem Soc (2003) 1.04
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins (2003) 1.03
Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations. Proteins (2002) 1.03
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J Chem Phys (2007) 1.02
Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir (2007) 1.00
Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations. J Am Chem Soc (2009) 1.00
Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane-domain formation. Biochemistry (2010) 0.98
Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys J (2010) 0.98
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins (2002) 0.98
Application of mean field boundary potentials in simulations of lipid vesicles. J Phys Chem B (2008) 0.98
Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B (2013) 0.97
A single bicontinuous cubic phase induced by fusion peptides. J Am Chem Soc (2009) 0.96
Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discuss (2013) 0.96
Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.96
Molecular view of the role of fusion peptides in promoting positive membrane curvature. J Am Chem Soc (2012) 0.95
Molecular dynamics study of the folding of hydrophobin SC3 at a hydrophilic/hydrophobic interface. Biophys J (2002) 0.94
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Sci (2004) 0.93
Calculation of the redox potential of the protein azurin and some mutants. Chembiochem (2005) 0.93
The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. J Mol Biol (2008) 0.93
Computationally designed libraries for rapid enzyme stabilization. Protein Eng Des Sel (2014) 0.92
Lipid acrobatics in the membrane fusion arena. Curr Top Membr (2011) 0.92
Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins (2002) 0.91
Structural investigation of MscL gating using experimental data and coarse grained MD simulations. PLoS Comput Biol (2012) 0.91
The molecular basis for antimicrobial activity of pore-forming cyclic peptides. Biophys J (2011) 0.91
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J Comput Aided Mol Des (2010) 0.90
Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool. J Biol Chem (2012) 0.90
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J Comput Aided Mol Des (2014) 0.89
Protein shape change has a major effect on the gating energy of a mechanosensitive channel. Biophys J (2011) 0.89
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail. J Am Chem Soc (2006) 0.89
Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. J Phys Chem B (2009) 0.89
Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discuss (2013) 0.89
Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models" by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Phys Chem Chem Phys (2010) 0.87
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. J Biomol NMR (2002) 0.87
Charge group partitioning in biomolecular simulation. J Comput Biol (2013) 0.87
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem (2007) 0.86
Enantioselective enzymes by computational design and in silico screening. Angew Chem Int Ed Engl (2015) 0.86
Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models. Proteins (2012) 0.86
Simulation studies of pore and domain formation in a phospholipid monolayer. J Chem Phys (2005) 0.86
Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation. Proteins (2010) 0.86
Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study. J Phys Chem B (2006) 0.85
Weak, strong, and coherent regimes of Fröhlich condensation and their applications to terahertz medicine and quantum consciousness. Proc Natl Acad Sci U S A (2009) 0.85
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study. Proteins (2008) 0.85
Incorporating the effect of ionic strength in free energy calculations using explicit ions. J Comput Chem (2005) 0.85
Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194. Biochim Biophys Acta (2011) 0.85