Published in Drug Discov Today on June 08, 2010
Evolutionary forces shaping the Golgi glycosylation machinery: why cell surface glycans are universal to living cells. Cold Spring Harb Perspect Biol (2011) 2.23
Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr Opin Struct Biol (2010) 1.00
Structural and energetic basis of carbohydrate-aromatic packing interactions in proteins. J Am Chem Soc (2013) 0.94
Carbohydrate force fields. Wiley Interdiscip Rev Comput Mol Sci (2012) 0.91
In silico-aided design of a glycan ligand of sialoadhesin for in vivo targeting of macrophages. J Am Chem Soc (2012) 0.90
Modification and periplasmic translocation of the biofilm exopolysaccharide poly-β-1,6-N-acetyl-D-glucosamine. Proc Natl Acad Sci U S A (2014) 0.86
Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PLoS One (2013) 0.85
Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. J Chem Theory Comput (2016) 0.81
Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology (2015) 0.81
Application of Metabolic 13C Labeling in Conjunction with High-Field Nuclear Magnetic Resonance Spectroscopy for Comparative Conformational Analysis of High Mannose-Type Oligosaccharides. Biomolecules (2013) 0.80
Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology. J Comput Aided Mol Des (2014) 0.80
Overexpression of a homogeneous oligosaccharide with 13C labeling by genetically engineered yeast strain. J Biomol NMR (2011) 0.79
The use of glycoinformatics in glycochemistry. Beilstein J Org Chem (2012) 0.79
Computational tools for epitope vaccine design and evaluation. Curr Opin Virol (2015) 0.79
Prediction of conformationally dependent atomic multipole moments in carbohydrates. J Comput Chem (2015) 0.78
Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol (2014) 0.78
Development and Application of Multidimensional HPLC Mapping Method for O-linked Oligosaccharides. Biomolecules (2011) 0.78
Structural and functional roles of glycosylation in fungal laccase from Lentinus sp. PLoS One (2015) 0.77
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des (2017) 0.75
Residue-centric modeling and design of saccharide and glycoconjugate structures. J Comput Chem (2016) 0.75
Assessment of Pasteurella multocida A Lipopolysaccharide, as an Adhesin in an In Vitro Model of Rabbit Respiratory Epithelium. Vet Med Int (2017) 0.75
Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics, and nuclear magnetic resonance. Biomed Res Int (2014) 0.75
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
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
Biological roles of oligosaccharides: all of the theories are correct. Glycobiology (1993) 12.38
Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J (2004) 8.19
Dynamics of folded proteins. Nature (1977) 7.82
Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68
Empirical force fields for biological macromolecules: overview and issues. J Comput Chem (2004) 7.49
Receptor determinants of human and animal influenza virus isolates: differences in receptor specificity of the H3 hemagglutinin based on species of origin. Virology (1983) 7.26
The sweet and sour of cancer: glycans as novel therapeutic targets. Nat Rev Cancer (2005) 5.98
The many roles of computation in drug discovery. Science (2004) 5.66
The impact of glycosylation on the biological function and structure of human immunoglobulins. Annu Rev Immunol (2007) 4.96
Glycobiology: Toward Understanding the Function of Sugars. Chem Rev (1996) 4.93
GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem (2008) 4.51
Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1. Cell (2000) 3.95
Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature (2008) 3.79
Aberrant glycosylation in tumors and tumor-associated carbohydrate antigens. Adv Cancer Res (1989) 3.25
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Solvent interactions determine carbohydrate conformation. Proc Natl Acad Sci U S A (2001) 3.12
Use of targeted glycoproteomics to identify serum glycoproteins that correlate with liver cancer in woodchucks and humans. Proc Natl Acad Sci U S A (2005) 2.70
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. Annu Rev Biochem (1986) 2.61
Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem (2002) 2.49
Engineering galactose-binding activity into a C-type mannose-binding protein. Nature (1992) 2.29
Solvated ensemble averaging in the calculation of partial atomic charges. J Comput Chem (2001) 2.02
Update and perspectives on congenital disorders of glycosylation. Glycobiology (2001) 1.94
Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers. J Chem Theory Comput (2007) 1.88
Automated conformational energy fitting for force-field development. J Mol Model (2008) 1.84
Carbohydrates as future anti-adhesion drugs for infectious diseases. Biochim Biophys Acta (2006) 1.75
Combining docking and molecular dynamic simulations in drug design. Med Res Rev (2006) 1.70
The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity. Nat Struct Mol Biol (2004) 1.66
Lectin structure. Annu Rev Biophys Biomol Struct (1995) 1.65
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. J Comput Chem (2005) 1.51
Structural basis of trimannoside recognition by concanavalin A. J Biol Chem (1996) 1.51
Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev (2000) 1.48
Aberrant glycosylation in IgA nephropathy (IgAN). Kidney Int (2004) 1.46
A new GROMOS force field for hexopyranose-based carbohydrates. J Comput Chem (2005) 1.45
Carbohydrate-pi interactions: what are they worth? J Am Chem Soc (2008) 1.41
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates. Theochem (2000) 1.36
Thermodynamics of monosaccharide binding to concanavalin A, pea (Pisum sativum) lectin, and lentil (Lens culinaris) lectin. J Biol Chem (1993) 1.32
Gaussian induced dipole polarization model. J Comput Chem (2007) 1.28
Polarizable Force Fields: History, Test Cases, and Prospects. J Chem Theory Comput (2007) 1.27
Structural glycobiology: a game of snakes and ladders. Glycobiology (2008) 1.25
Correlated C-C and C-O bond conformations in saccharide hydroxymethyl groups: parametrization and application of redundant 1H-1H, 13C-1H, and 13C-13C NMR J-couplings. J Am Chem Soc (2004) 1.23
An improved OPLS-AA force field for carbohydrates. J Comput Chem (2002) 1.20
Targeted glycoproteomic identification of biomarkers for human breast carcinoma. J Proteome Res (2008) 1.14
Progress towards the development of a HIV-1 gp41-directed vaccine. Curr HIV Res (2004) 1.13
Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J Am Chem Soc (2008) 1.13
Carbohydrate-carbohydrate interactions in cell recognition. Curr Opin Struct Biol (2004) 1.13
Thermodynamics of oligosaccharide binding to a monoclonal antibody specific for a Salmonella O-antigen point to hydrophobic interactions in the binding site. J Biol Chem (1992) 1.12
New trends in carbohydrate-based vaccines. Drug Discov Today Technol (2004) 1.11
Alcohols, ethers, carbohydrates, and related compounds. IV. Carbohydrates. J Comput Chem (2003) 1.11
Energetics of lectin-carbohydrate binding. A microcalorimetric investigation of concanavalin A-oligomannoside complexation. J Biol Chem (1992) 1.09
Three-dimensional structures of oligosaccharides. Curr Opin Struct Biol (1995) 1.09
Atoms in molecules interpretation of the anomeric effect in the O--C--O unit. J Comput Chem (2007) 1.09
Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae. Proc Natl Acad Sci U S A (2006) 1.04
Altered glycosylation of proteins in cancer: what is the potential for new anti-tumour strategies. Anticancer Agents Med Chem (2008) 1.04
Carbohydrate-protein recognition: molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A. Biophys J (2001) 1.03
Solution conformation of alpha D(1-3)- and alpha D(1-6)-linked oligomannosides using proton nuclear magnetic resonance. Biochemistry (1983) 1.03
Potential energy functions. Curr Opin Struct Biol (1995) 1.02
Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: the role of sialic acid. Carbohydr Res (2005) 1.00
Tumor-associated carbohydrate antigens: a possible avenue for cancer prevention. Immunol Cell Biol (2005) 0.99
Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc (2009) 0.97
Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids. Mol Simul (2008) 0.97
Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc (2006) 0.96
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces. Glycobiology (2008) 0.96
Reconciling solvent effects on rotamer populations in carbohydrates - A joint MD and NMR analysis. Can J Chem (2006) 0.95
Bacterium-host protein-carbohydrate interactions and pathogenicity. Biochem Soc Trans (1999) 0.93
A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem (2008) 0.93
Brain-directed gene therapy for lysosomal storage disease: going well beyond the blood- brain barrier. Proc Natl Acad Sci U S A (2002) 0.93
BALLDock/SLICK: a new method for protein-carbohydrate docking. J Chem Inf Model (2008) 0.92
Current topics in computer-aided drug design. J Pharm Sci (2008) 0.92
Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. J Biomol NMR (2009) 0.90
TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations. J Chem Theory Comput (2007) 0.89
Conformational epitope of the type III group B Streptococcus capsular polysaccharide. J Immunol (1999) 0.89
Carbohydrate moieties as vaccine candidates. Clin Infect Dis (2005) 0.88
Energetics of carbohydrate binding by a 14 kDa S-type mammalian lectin. Biochem J (1995) 0.88
Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations. J Biol Chem (2005) 0.88
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance. J Comput Aided Mol Des (2006) 0.87
Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comput Chem (2003) 0.87
Minimum chemical requirements for adhesin activity of the acid-stable part of Candida albicans cell wall phosphomannoprotein complex. Infect Immun (1998) 0.87
Alcohols, ethers, carbohydrates, and related compounds. III. The 1,2-dimethoxyethane system. J Comput Chem (2003) 0.86
Contribution of ligand desolvation to binding thermodynamics in a ligand-protein interaction. Angew Chem Int Ed Engl (2006) 0.86
On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J Phys Chem A (2008) 0.86
A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II. Biochemistry (2005) 0.85
Antithrombin III phenylalanines 122 and 121 contribute to its high affinity for heparin and its conformational activation. J Biol Chem (2003) 0.84
Molecular diversity through sugar scaffolds. Drug Discov Today (2003) 0.84
Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect. J Comput Chem (2003) 0.84
Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. J Phys Chem B (2009) 0.83
Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides. Proteins (2008) 0.83
Modeling protein recognition of carbohydrates. Proteins (2005) 0.82
Elucidation of the mechanism of interaction of sheep spleen galectin-1 with splenocytes and its role in cell-matrix adhesion. J Mol Recognit (2000) 0.82
Binding sub-site dissection of a carbohydrate-binding module reveals the contribution of entropy to oligosaccharide recognition at "non-primary" binding subsites. J Mol Biol (2004) 0.80
A QM/MM analysis of the conformations of crystalline sucrose moieties. Carbohydr Res (2000) 0.79
Conformational behaviour of glycomimetics: NMR and molecular modelling studies of the C-glycoside analogue of the disaccharide methyl beta-D-galactopyranosyl-(1-->3)-beta-D-glucopyranoside. Carbohydr Res (2007) 0.78
New sialyl Lewis(x) mimic containing an alpha-substituted beta(3)-amino acid spacer. Carbohydr Res (2007) 0.77
Solution-state conformational study of the hevamine inhibitor allosamidin and six potential inhibitor analogues by NMR spectroscopy and molecular modeling. J Org Chem (2002) 0.76
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem (2008) 4.51
Effects of glycosylation on peptide conformation: a synergistic experimental and computational study. J Am Chem Soc (2004) 1.37
Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J Am Soc Mass Spectrom (2008) 1.36
Gaussian induced dipole polarization model. J Comput Chem (2007) 1.28
Structural glycobiology: a game of snakes and ladders. Glycobiology (2008) 1.25
Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J Am Chem Soc (2008) 1.13
The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proc Biol Sci (2008) 1.12
Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity. Proteins (2003) 1.09
Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae. Proc Natl Acad Sci U S A (2006) 1.04
The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. J Biol Chem (2001) 1.04
Enzymatic basis for N-glycan sialylation: structure of rat α2,6-sialyltransferase (ST6GAL1) reveals conserved and unique features for glycan sialylation. J Biol Chem (2013) 1.01
Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: the role of sialic acid. Carbohydr Res (2005) 1.00
A hydration study of (1-->4) and (1-->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. J Comput Chem (2004) 0.99
From agonist to antagonist: structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol Immunol (2011) 0.97
Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids. Mol Simul (2008) 0.97
Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc (2006) 0.96
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces. Glycobiology (2008) 0.96
Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting. Anal Chem (2009) 0.95
Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement. J Am Chem Soc (2010) 0.94
Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One (2013) 0.93
Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. J Comput Chem (2013) 0.92
Presentation, presentation, presentation! Molecular-level insight into linker effects on glycan array screening data. Glycobiology (2013) 0.91
The conformational properties of methyl alpha-(2,8)-di/trisialosides and their N-acyl analogues: implications for anti-Neisseria meningitidis B vaccine design. Biochemistry (2008) 0.90
Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac{alpha}2-6Gal{beta}1-4GlcNAc human-type influenza receptor. Glycobiology (2011) 0.89
On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J Phys Chem A (2008) 0.86
Unraveling cellulose microfibrils: a twisted tale. Biopolymers (2013) 0.83
Carbohydrate recognition by an architecturally complex α-N-acetylglucosaminidase from Clostridium perfringens. PLoS One (2012) 0.82
Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides. J Phys Chem B (2012) 0.82
The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop. PLoS One (2013) 0.82
Quantifying the role of water in protein-carbohydrate interactions. J Phys Chem A (2003) 0.82
Inhibition of Golgi mannosidase II with mannostatin A analogues: synthesis, biological evaluation, and structure-activity relationship studies. Chembiochem (2004) 0.82
Fourier transform mass spectrometry to monitor hyaluronan-protein interactions: use of hydrogen/deuterium amide exchange. Rapid Commun Mass Spectrom (2007) 0.81
Molecular recognition of Candida albicans (1->2)-β-mannan oligosaccharides by a protective monoclonal antibody reveals the immunodominance of internal saccharide residues. J Biol Chem (2012) 0.81
Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline. BMC Evol Biol (2014) 0.79
Investigating changes in the gas-phase conformation of Antithrombin III upon binding of Arixtra using traveling wave ion mobility spectrometry (TWIMS). Analyst (2015) 0.79
BFMP: a method for discretizing and visualizing pyranose conformations. J Chem Inf Model (2014) 0.78
The structure and conformational behavior of sulfonium salt glycosidase inhibitors in solution: a combined quantum mechanical NMR approach. J Am Chem Soc (2004) 0.78
New sialyl Lewis(x) mimic containing an alpha-substituted beta(3)-amino acid spacer. Carbohydr Res (2007) 0.77
Calculating binding free energies for protein-carbohydrate complexes. Methods Mol Biol (2015) 0.77
Defining the structural origin of the substrate sequence independence of O-GlcNAcase using a combination of molecular docking and dynamics simulation. Glycobiology (2013) 0.77
Sugar-modified foldamers as conformationally defined and biologically distinct glycopeptide mimics. Angew Chem Int Ed Engl (2013) 0.77
Specificity of furanoside-protein recognition through antibody engineering and molecular modeling. Chemistry (2014) 0.75