Published in J Mol Biol on September 25, 2010
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem (2014) 1.89
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CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
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Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J Comput Chem (2007) 1.86
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Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophys J (2005) 1.37
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J Struct Biol (2003) 1.36
Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study. Biophys J (2008) 1.34
Self-guided Langevin dynamics study of regulatory interactions in NtrC. Proteins (2009) 1.32
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Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J (2002) 1.30
Dynamical motions of lipids and a finite size effect in simulations of bilayers. J Chem Phys (2006) 1.30
Protein conformational transitions explored by mixed elastic network models. Proteins (2007) 1.26
Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. J Comput Chem (2009) 1.24
Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J Am Chem Soc (2002) 1.23
Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions. Biophys J (2002) 1.21
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys J (2005) 1.20
Multiscale methods for macromolecular simulations. Curr Opin Struct Biol (2008) 1.19
Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. J Mol Biol (2007) 1.15
Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems. J Chem Phys (2008) 1.14
Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water. Biophys J (2004) 1.13
Update of the cholesterol force field parameters in CHARMM. J Phys Chem B (2011) 1.12
Annealing function of GroEL: structural and bioinformatic analysis. Biophys Chem (2003) 1.10
Toward canonical ensemble distribution from self-guided Langevin dynamics simulation. J Chem Phys (2011) 1.08
Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B (2010) 1.07
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pH replica-exchange method based on discrete protonation states. Proteins (2011) 1.04
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Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophys J (2013) 1.01
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Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins (2007) 1.01
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An improved method for nonbonded list generation: rapid determination of near-neighbor pairs. J Comput Chem (2003) 1.00
Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophys J (2006) 0.99
CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. J Chem Inf Model (2013) 0.99
A computational characterization of boron-oxygen multiple bonding in HN=CH-CH=CH-NH-BO. J Phys Chem A (2008) 0.99
Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations. J Mol Biol (2005) 0.97
Development of small molecules designed to modulate protein-protein interactions. J Comput Aided Mol Des (2006) 0.97
Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein. Proc Natl Acad Sci U S A (2007) 0.96
Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy. J Biol Chem (2005) 0.96
Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble. J Chem Phys (2011) 0.96
Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms. J Phys Chem A (2007) 0.95
Structure of the boronic acid dimer and the relative stabilities of its conformers. J Phys Chem A (2006) 0.95
Protein recognition motifs: design of peptidomimetics of helix surfaces. Biopolymers (2007) 0.95
Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. J Phys Chem B (2009) 0.95
A computational investigation of the geometrical structure and protodeboronation of boroglycine, H2N-CH2-B(OH)2. J Phys Chem A (2007) 0.91
Identifying natural substrates for chaperonins using a sequence-based approach. Protein Sci (2004) 0.91
Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophys J (2012) 0.90
Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. J Am Chem Soc (2002) 0.90
Binding and release of cholesterol in the Osh4 protein of yeast. Proteins (2009) 0.90
Mesoscale inhomogeneities in aqueous solutions of small amphiphilic molecules. Faraday Discuss (2013) 0.89
Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles. Structure (2011) 0.89
MSCALE: A General Utility for Multiscale Modeling. J Chem Theory Comput (2011) 0.87
Maintain rigid structures in Verlet based cartesian molecular dynamics simulations. J Chem Phys (2012) 0.87
Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure (2012) 0.87
ST-analyzer: a web-based user interface for simulation trajectory analysis. J Comput Chem (2014) 0.86
Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain. Biochim Biophys Acta (2012) 0.86
Computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, Using H2O and H2O2. J Phys Chem A (2009) 0.86
Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. J Comput Chem (2012) 0.86
Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran. J Am Chem Soc (2008) 0.86
Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. J Phys Chem B (2014) 0.86
The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. J Comput Chem (2011) 0.86
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. J Comput Aided Mol Des (2011) 0.85
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. J Comput Aided Mol Des (2014) 0.85
Lipid chain branching at the iso- and anteiso-positions in complex Chlamydia membranes: a molecular dynamics study. Biochim Biophys Acta (2010) 0.84
Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex. Structure (2008) 0.84
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Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. J Comput Chem (2012) 0.83
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A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. J Pharm Sci (2004) 0.83
Membrane-binding mechanism of a peripheral membrane protein through microsecond molecular dynamics simulations. J Mol Biol (2012) 0.82
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Modeling of the major gas vesicle protein, GvpA: from protein sequence to vesicle wall structure. J Struct Biol (2012) 0.82
Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling. J Chem Phys (2012) 0.82
CHARMM36 united atom chain model for lipids and surfactants. J Phys Chem B (2014) 0.81
Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Curr Protein Pept Sci (2009) 0.81
Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. J Struct Biol (2013) 0.80
A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes. Biol Direct (2008) 0.80
Lipopolysaccharide membrane building and simulation. Methods Mol Biol (2015) 0.80
Lipid membranes with a majority of cholesterol: applications to the ocular lens and aquaporin 0. J Phys Chem B (2011) 0.80
Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide. J Phys Chem Lett (2011) 0.80