Published in Methods Mol Biol on January 01, 2015
BamA POTRA Domain Interacts with a Native Lipid Membrane Surface. Biophys J (2016) 0.81
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophys J (2016) 0.81
Permeability Barrier of Gram-Negative Cell Envelopes and Approaches To Bypass It. ACS Infect Dis (2016) 0.80
Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophys J (2016) 0.76
Refinement of OprH-LPS Interactions by Molecular Simulations. Biophys J (2017) 0.75
Pathogen recognition and innate immunity. Cell (2006) 44.14
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
Biosynthesis and assembly of capsular polysaccharides in Escherichia coli. Annu Rev Biochem (2006) 5.41
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One (2007) 2.65
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys J (2006) 2.30
The structures of Escherichia coli O-polysaccharide antigens. FEMS Microbiol Rev (2006) 2.13
Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol (2008) 1.86
Computer simulations of membrane proteins. Biochim Biophys Acta (2004) 1.71
A single nucleotide exchange in the wzy gene is responsible for the semirough O6 lipopolysaccharide phenotype and serum sensitivity of Escherichia coli strain Nissle 1917. J Bacteriol (2002) 1.66
Molecular dynamics simulations of proteins in lipid bilayers. Curr Opin Struct Biol (2005) 1.62
Molecular simulation approaches to membrane proteins. Structure (2011) 1.52
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Development of the CHARMM Force Field for Lipids. J Phys Chem Lett (2011) 1.29
Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa. Biophys J (2001) 1.23
Structural studies on the short-chain lipopolysaccharide of Vibrio cholerae O139 Bengal. Eur J Biochem (1997) 1.01
Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation. Proteins (2009) 0.87
Structural studies of the Escherichia coli O-antigen 6. Carbohydr Res (1984) 0.86
Structural studies utilizing 13C-enrichment of the O-antigen polysaccharide from the enterotoxigenic Escherichia coli O159 cross-reacting with Shigella dysenteriae type 4. Eur J Biochem (1999) 0.80
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
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83
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
Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J (2005) 2.84
Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties. J Am Chem Soc (2002) 2.76
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
Polarizable empirical force field for alkanes based on the classical Drude oscillator model. J Phys Chem B (2005) 2.56
Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs. Cell (2011) 2.55
Theoretical and computational models of biological ion channels. Q Rev Biophys (2004) 2.41
The structures of Escherichia coli O-polysaccharide antigens. FEMS Microbiol Rev (2006) 2.13
Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys (2004) 2.00
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol (2002) 1.95
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
Automated conformational energy fitting for force-field development. J Mol Model (2008) 1.84
CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem (2013) 1.82
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A (2002) 1.78
The structure of aqueous guanidinium chloride solutions. J Am Chem Soc (2004) 1.66
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Computational fragment-based binding site identification by ligand competitive saturation. PLoS Comput Biol (2009) 1.61
Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B (2008) 1.57
Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH. J Mol Biol (2007) 1.53
Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran. Biophys J (2007) 1.48
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem (2005) 1.48
Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants. J Org Chem (2002) 1.44
Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction. J Med Chem (2004) 1.41
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J (2002) 1.40
CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model (2008) 1.38
Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comput Sci (2003) 1.37
Brucellosis vaccines: assessment of Brucella melitensis lipopolysaccharide rough mutants defective in core and O-polysaccharide synthesis and export. PLoS One (2008) 1.37
2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists. J Am Chem Soc (2003) 1.36
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36
Transmembrane helix tilting: insights from calculating the potential of mean force. Phys Rev Lett (2008) 1.35
Computational approaches for investigating base flipping in oligonucleotides. Chem Rev (2006) 1.35
Is arginine charged in a membrane? Biophys J (2007) 1.33
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J Comput Chem (2002) 1.32
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
A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep (2013) 1.28
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity. J Med Chem (2007) 1.22
Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem (2012) 1.20
Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol (2008) 1.19
Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency. Mol Immunol (2010) 1.18
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J Comput Chem (2007) 1.18
All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo. PLoS One (2012) 1.15
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J (2012) 1.15
Computational identification of inhibitors of protein-protein interactions. Curr Top Med Chem (2007) 1.14
Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc (2004) 1.14
EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology (2010) 1.13
Update of the cholesterol force field parameters in CHARMM. J Phys Chem B (2011) 1.12
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR (2005) 1.12
CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B (2010) 1.12
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J (2012) 1.12
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol (2010) 1.11
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model (2013) 1.09
Divalent metal ion complexes of S100B in the absence and presence of pentamidine. J Mol Biol (2008) 1.09
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
Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. J Med Chem (2004) 1.07
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B (2010) 1.07
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
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Proc Natl Acad Sci U S A (2012) 1.05
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res (2003) 1.05
Atomistic view of base flipping in DNA. Philos Trans A Math Phys Eng Sci (2004) 1.05
Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J Phys Chem B (2005) 1.04
The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer (2013) 1.04
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res (2004) 1.03
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
Structural analysis of glycans by NMR chemical shift prediction. Anal Chem (2011) 1.01
Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol (2009) 1.01
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B (2013) 1.01
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol (2009) 1.01
Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. Biophys J (2011) 1.00
Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophys J (2011) 1.00
Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J Mol Biol (2005) 1.00
A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations. J Phys Chem B (2005) 0.99
CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. J Chem Inf Model (2013) 0.99
Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydr Res (2003) 0.98
Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors. Org Biomol Chem (2012) 0.98
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J (2011) 0.98