Bioinformatics and molecular modeling in glycobiology

[1]  M. Kanehisa,et al.  An improved scoring scheme for predicting glycan structures from gene expression data. , 2007, Genome informatics. International Conference on Genome Informatics.

[2]  J. Marth,et al.  Mammalian glycosylation in immunity , 2008, Nature Reviews Immunology.

[3]  R. Boelens,et al.  The structural basis of the difference in sensitivity for PNGase F in the de-N-glycosylation of the native bovine pancreatic ribonucleases B and BS. , 2008, Biochemistry.

[4]  N. Null.  The IUPAC International Chemical Identifier (InChI) , 2009 .

[5]  Austin B. Yongye,et al.  The conformational properties of methyl alpha-(2,8)-di/trisialosides and their N-acyl analogues: implications for anti-Neisseria meningitidis B vaccine design. , 2008, Biochemistry.

[6]  Yan Liu,et al.  Carbohydrate microarrays: key developments in glycobiology , 2009, Biological chemistry.

[7]  Claus-Wilhelm von der Lieth,et al.  GlyProt: in silico glycosylation of proteins , 2005, Nucleic Acids Res..

[8]  J. Turnbull,et al.  Saccharide microarrays for high-throughput interrogation of glycan-protein binding interactions. , 2009, Methods in molecular biology.

[9]  A. McNaught,et al.  NOMENCLATURE OF CARBOHYDRATES (Recommendations 1996) , 1997 .

[10]  Alessio Ceroni,et al.  Characterizing the glycome of the mammalian immune system , 2008, Immunology and cell biology.

[11]  R. Dror,et al.  Long-timescale molecular dynamics simulations of protein structure and function. , 2009, Current opinion in structural biology.

[12]  B. Shoichet,et al.  Molecular docking and ligand specificity in fragment-based inhibitor discovery. , 2009, Nature chemical biology.

[13]  David Goldberg,et al.  Automated N-glycopeptide identification using a combination of single- and tandem-MS. , 2007, Journal of proteome research.

[14]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[15]  Wayne B. Bosma,et al.  DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose. , 2009, Carbohydrate research.

[16]  John A. Miller,et al.  Integration of Glycomics Knowledge and Data , 2010 .

[17]  A. Imberty,et al.  Data bank of three-dimensional structures of disaccharides, a tool to build 3-D structures of oligosaccharides , 2005, Glycoconjugate Journal.

[18]  M. Bäckström,et al.  High-throughput and high-sensitivity nano-LC/MS and MS/MS for O-glycan profiling. , 2009, Methods in molecular biology.

[19]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[20]  Sarah M. Tschampel,et al.  TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations. , 2007, Journal of chemical theory and computation.

[21]  J. Gready,et al.  Combining docking and molecular dynamic simulations in drug design , 2006, Medicinal research reviews.

[22]  J. Paulson,et al.  Glycomics: an integrated systems approach to structure-function relationships of glycans , 2005, Nature Methods.

[23]  R Apweiler,et al.  On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. , 1999, Biochimica et biophysica acta.

[24]  Gert Matthijs,et al.  Congenital disorders of glycosylation: a rapidly expanding disease family. , 2007, Annual review of genomics and human genetics.

[25]  Martin Frank,et al.  Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. , 2009, Glycobiology.

[26]  Stephen Hanessian,et al.  Docking of aminoglycosides to hydrated and flexible RNA. , 2006, Journal of medicinal chemistry.

[27]  G. Jiménez‐Osés,et al.  Insights into the geometrical features underlying beta-O-GlcNAc glycosylation: water pockets drastically modulate the interactions between the carbohydrate and the peptide backbone. , 2009, Chemistry.

[28]  P. Seeberger.  Chemical glycobiology: why now? , 2009, Nature chemical biology.

[29]  M. Frank,et al.  Synergy of Computational and Experimental Methods in Carbohydrate 3D Structure Determination and Validation , 2009 .

[30]  Hildegard Geyer,et al.  Strategies for analysis of glycoprotein glycosylation. , 2006, Biochimica et biophysica acta.

[31]  A. Strang.  Letter to the Glyco-Forum , 1998 .

[32]  Toshisuke Kawasaki,et al.  GlycoEpitope: the Integrated Database of Carbohydrate Antigens and Antibodies , 2006 .

[33]  Alessio Ceroni,et al.  GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. , 2008, Journal of proteome research.

[34]  David J. Harvey,et al.  HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software. , 2008, Analytical biochemistry.

[35]  J. Hirabayashi,et al.  Frontal affinity chromatography: sugar–protein interactions , 2007, Nature Protocols.

[36]  W. Hull,et al.  A (Critical) Survey of Modeling Protocols Used to Explore the Conformational Space of Oligosaccharides , 1997 .

[37]  Thomas Lütteke,et al.  Biological Crystallography Analysis and Validation of Carbohydrate Three-dimensional Structures , 2022 .

[38]  G. P. Johnson,et al.  The external-anomeric torsional effect. , 2005, Carbohydrate research.

[39]  S. Vandenbussche,et al.  Aromatic-carbohydrate interactions: an NMR and computational study of model systems. , 2008, Chemistry.

[40]  Niclas G Karlsson,et al.  Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data , 2004, Proteomics.

[41]  Austin B. Yongye,et al.  Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids , 2008, Molecular simulation.

[42]  E. Damme.  Handbook of plant lectins : properties and biomedical applications , 1998 .

[43]  J E Bailey,et al.  A mathematical model of N-linked glycoform biosynthesis. , 1997, Biotechnology and bioengineering.

[44]  C. W. von der Lieth,et al.  Conformational analysis of the neutral exopolysaccharide produced by Lactobacillus delbrueckii ssp. bulgaricus LBB.B26. , 2009, Organic & biomolecular chemistry.

[45]  Yoshihiro Yamanishi,et al.  Extraction of leukemia specific glycan motifs in humans by computational glycomics. , 2005, Carbohydrate research.

[46]  A. Bairoch,et al.  Annotation of glycoproteins in the SWISS-PROT database. , 2001, Proteomics.

[47]  P Bork,et al.  Automated annotation of GPI anchor sites: case study C. elegans. , 2000, Trends in biochemical sciences.

[48]  Martin Frank,et al.  Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts , 2003, Journal of molecular modeling.

[49]  Kiyoko F. Aoki-Kinoshita,et al.  Bioinformatics approaches in glycomics and drug discovery. , 2006, Current opinion in molecular therapeutics.

[50]  Henry S. Rzepa,et al.  Communication and re-use of chemical information in bioscience , 2005, BMC Bioinformatics.

[51]  O. Lund,et al.  NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility , 1998, Glycoconjugate Journal.

[52]  Nicolle H. Packer,et al.  GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources , 2001, Nucleic Acids Res..

[53]  G J Davies,et al.  A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. , 1997, The Biochemical journal.

[54]  David F. Smith,et al.  Glycan-Binding Proteins and Glycan Microarrays , 2010 .

[55]  Xianghong Qian,et al.  The effects of water on beta-D-xylose condensation reactions. , 2009, The journal of physical chemistry. A.

[56]  Catherine Brooksbank,et al.  The European Bioinformatics Institute’s data resources , 2009, Nucleic Acids Res..

[57]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[58]  J. Hirabayashi.  Lectin-based structural glycomics: Glycoproteomics and glycan profiling , 2004, Glycoconjugate Journal.

[59]  Jesús Jiménez-Barbero,et al.  NMR spectroscopy of glycoconjugates , 2002 .

[60]  S. Pérez.  2.11 – Molecular Modeling in Glycoscience , 2007 .

[61]  S B Engelsen,et al.  A molecular builder for carbohydrates: application to polysaccharides and complex carbohydrates. , 1998, Biopolymers.

[62]  R. Laine,et al.  A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 x 10(12) structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems. , 1994, Glycobiology.

[63]  H. Perreault,et al.  Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[64]  Huijuan Li,et al.  Pharmacological significance of glycosylation in therapeutic proteins. , 2009, Current opinion in biotechnology.

[65]  Joseph Zaia,et al.  Mass spectrometry and the emerging field of glycomics. , 2008, Chemistry & biology.

[66]  Computer Corner,et al.  Automated annotation of GPI anchor sites: case study , 2000 .

[67]  Yanli Wang,et al.  PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..

[68]  M. Kanehisa,et al.  Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. , 2003, Journal of the American Chemical Society.

[69]  Alexander D. MacKerell,et al.  CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. , 2009, Journal of chemical theory and computation.

[70]  Rolf Apweiler,et al.  Linking publication, gene and protein data , 2006, Nature Cell Biology.

[71]  M. Frank,et al.  Bioinformatics for Glycobiology and Glycomics , 2009 .

[72]  Martin Frank,et al.  Bioinformatics for glycomics: Status, methods, requirements and perspectives , 2004, Briefings Bioinform..

[73]  A. Sytkowski,et al.  Erythropoietin: new approaches to improved molecular designs and therapeutic alternatives. , 2008, Current pharmaceutical design.

[74]  C. W. von der Lieth,et al.  Conformational structure of some trimeric and pentameric structural units of heparin. , 2007, The journal of physical chemistry. A.

[75]  Vojtech Spiwok,et al.  Conformational free energy surface of alpha-N-acetylneuraminic acid: an interplay between hydrogen bonding and solvation. , 2009, The journal of physical chemistry. B.

[76]  L. Mahal.  Glycomics: towards bioinformatic approaches to understanding glycosylation. , 2008, Anti-cancer agents in medicinal chemistry.

[77]  Louise Royle,et al.  Proposal for a standard system for drawing structural diagrams of N‐ and O‐linked carbohydrates and related compounds , 2009, Proteomics.

[78]  D. Ashline,et al.  Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MSn data. , 2005, Analytical chemistry.

[79]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[80]  Sai Kumar Ramadugu,et al.  When sugars get wet. A comprehensive study of the behavior of water on the surface of oligosaccharides. , 2009, The journal of physical chemistry. B.

[81]  Robert J Woods,et al.  Reconciling solvent effects on rotamer populations in carbohydrates - A joint MD and NMR analysis. , 2006, Canadian journal of chemistry.

[82]  René Ranzinger,et al.  Exploring the structural diversity of mammalian carbohydrates ("glycospace") by statistical databank analysis. , 2007, ACS chemical biology.

[83]  Haixu Tang,et al.  Automated interpretation of MS/MS spectra of oligosaccharides , 2005, ISMB.

[84]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[85]  Michel Schneider,et al.  UniProtKB/Swiss-Prot. , 2007, Methods in molecular biology.

[86]  Alessio Ceroni,et al.  The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures , 2007, Source Code for Biology and Medicine.

[87]  Raymond A Dwek,et al.  Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. , 2003, Glycobiology.

[88]  Hiroyuki Kaji,et al.  Proteomics Reveals N-Linked Glycoprotein Diversity in Caenorhabditis elegans and Suggests an Atypical Translocation Mechanism for Integral Membrane Proteins*S , 2007, Molecular & Cellular Proteomics.

[89]  Jonathan D. Hirst,et al.  Prediction of glycosylation sites using random forests , 2008, BMC Bioinformatics.

[90]  Ziding Zhang,et al.  Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs , 2008, BMC Bioinformatics.

[91]  Louise Royle,et al.  Separation‐based Glycoprofiling Approaches using Fluorescent Labels , 2007, Proteomics.

[92]  Thomas Lütteke,et al.  Web Resources for the Glycoscientist , 2008, Chembiochem : a European journal of chemical biology.

[93]  Julian Tirado-Rives,et al.  Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[94]  Antje Chang,et al.  BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 , 2008, Nucleic Acids Res..

[95]  Lakshmi Krishnamoorthy,et al.  Glycomic analysis: an array of technologies. , 2009, ACS chemical biology.

[96]  Susumu Goto,et al.  Prediction of glycan structures from gene expression data based on glycosyltransferase reactions , 2005, Bioinform..

[97]  David I. Stuart,et al.  Building meaningful models of glycoproteins , 2007, Nature Structural &Molecular Biology.

[98]  Emmanuel Maes,et al.  SOACS index: an easy NMR-based query for glycan retrieval. , 2009, Carbohydrate research.

[99]  R. Woods,et al.  Involvement of water in carbohydrate-protein binding: concanavalin A revisited. , 2008, Journal of the American Chemical Society.

[100]  Alain Laederach,et al.  Modeling protein recognition of carbohydrates , 2005, Proteins.

[101]  Richard D Cummings,et al.  Symbol nomenclature for glycan representation , 2009, Proteomics.

[102]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[103]  J. Peter-Katalinic,et al.  Software platform for high-throughput glycomics. , 2009, Analytical chemistry.

[104]  Kiyoko F. Aoki-Kinoshita,et al.  Frontiers in glycomics: Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11–13, 2006) , 2008, Proteomics.

[105]  S. Withers,et al.  Teaching old enzymes new tricks: engineering and evolution of glycosidases and glycosyl transferases for improved glycoside synthesis. , 2008, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[106]  Pierre-Nicholas Roy,et al.  Conformational Studies of Methyl β-d-Arabinofuranoside Using the AMBER/GLYCAM Approach. , 2009, Journal of chemical theory and computation.

[107]  C A Stortz,et al.  Disaccharide conformational maps: how adiabatic is an adiabatic map? , 1999, Carbohydrate research.

[108]  N. Okimoto,et al.  Prediction of the Structure of Complexes Comprised of Proteins and Glycosaminoglycans Using Docking Simulation and Cluster Analysis. , 2007, Journal of chemical theory and computation.

[109]  Claus-Wilhelm von der Lieth,et al.  GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages , 2007, Nucleic Acids Res..

[110]  James C Paulson,et al.  Frontiers in Glycomics; Bioinformatics and Biomarkers in Disease September 11‐13, 2006 Natcher Conference Center, NIH Campus, Bethesda, MD, USA , 2007, Proteomics.

[111]  G. Widmalm.  General NMR Spectroscopy of Carbohydrates and Conformational Analysis in Solution , 2021, Comprehensive Glycoscience.

[112]  P. Seeberger,et al.  Recent advances in carbohydrate-based vaccines. , 2009, Current opinion in chemical biology.

[113]  D. F. Green,et al.  Computational models explain the oligosaccharide specificity of cyanovirin‐N , 2008, Protein science : a publication of the Protein Society.

[114]  M. Eriksson,et al.  Differential effects of oligosaccharides on the hydration of simple cations. , 2008, The Journal of chemical physics.

[115]  J. Leary,et al.  STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry. , 2000, Analytical chemistry.

[116]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[117]  Phil Andrews,et al.  Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. , 2009, Journal of proteome research.

[118]  Oleg V Prezhdo,et al.  Atomistic simulation combined with analytic theory to study the response of the P-selectin/PSGL-1 complex to an external force. , 2009, The journal of physical chemistry. B.

[119]  A. Almond.  Biomolecular dynamics: Testing microscopic predictions against macroscopic experiments , 2006 .

[120]  C. Boudier,et al.  Antithrombin-binding Octasaccharides and Role of Extensions of the Active Pentasaccharide Sequence in the Specificity and Strength of Interaction , 2008, Journal of Biological Chemistry.

[121]  Dong Xu,et al.  Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. , 2009, Journal of molecular biology.

[122]  Martin Frank,et al.  Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB , 2004, Nucleic Acids Res..

[123]  Lutgarde Arckens,et al.  Sweet Substitute: A software tool for in silico fragmentation of peptide‐linked N‐glycans , 2004, Proteomics.

[124]  I. Tvaroška,et al.  The anomeric and exo-anomeric effects of a hydroxyl group and the stereochemistry of the hemiacetal linkage , 1998 .

[125]  E. Go,et al.  Simplification of mass spectral analysis of acidic glycopeptides using GlycoPep ID. , 2007, Analytical chemistry.

[126]  André M Deelder,et al.  Oligosaccharide analysis by graphitized carbon liquid chromatography–mass spectrometry , 2009, Analytical and bioanalytical chemistry.

[127]  Pauline M. Rudd,et al.  GlycoBase and autoGU: tools for HPLC-based glycan analysis , 2008, Bioinform..

[128]  William S York,et al.  GLYDE-an expressive XML standard for the representation of glycan structure. , 2005, Carbohydrate research.

[129]  Thomas Wetter,et al.  GlycomeDB – integration of open-access carbohydrate structure databases , 2008, BMC Bioinformatics.

[130]  Minoru Kanehisa,et al.  Mining significant tree patterns in carbohydrate sugar chains , 2008, ECCB.

[131]  R. Woods,et al.  Combining NMR and Simulation Methods in Oligosaccharide Conformational Analysis , 2003 .

[132]  Philip V. Toukach,et al.  Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de , 2007, Nucleic Acids Res..

[133]  Alan D. McNaught.  Nomenclature of carbohydrates , 1997 .

[134]  Martin Frank,et al.  Bioinformatics for glycobiology and glycomics : an introduction , 2009 .

[135]  Martin Frank,et al.  The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra. , 2006, Biochimica et biophysica acta.

[136]  Yaniv Altshuler,et al.  Glycoforum a Novel Linear Code ® Nomenclature for Complex Carbohydrates , 2022 .

[137]  Marshall W. Bern,et al.  Glycan family analysis for deducing N-glycan topology from single MS , 2009, Bioinform..

[138]  I Marchal,et al.  Bioinformatics in glycobiology. , 2003, Biochimie.

[139]  Yoshihiro Yamanishi,et al.  Glycan classification with tree kernels , 2007, Bioinform..

[140]  I. Tvaroška,et al.  Hybrid quantum mechanical/molecular mechanical investigation of the beta-1,4-galactosyltransferase-I mechanism. , 2009, The journal of physical chemistry. B.

[141]  Kiyoko F. Aoki-Kinoshita,et al.  KEGG as a glycome informatics resource. , 2006, Glycobiology.

[142]  G. Widmalm,et al.  Conformational flexibility and dynamics of two (1-->6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumour cells. , 2009, Chemistry.

[143]  Shin-Ichiro Nishimura,et al.  Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service , 2007, Nucleic Acids Res..

[144]  Wayne Boucher,et al.  The CCPN data model for NMR spectroscopy: Development of a software pipeline , 2005, Proteins.

[145]  David F. Burke,et al.  Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin , 2000, Nature.

[146]  M. Alan Chester,et al.  INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY AND INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY , 1997 .

[147]  Vojtech Spiwok,et al.  Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance , 2006, J. Comput. Aided Mol. Des..

[148]  Hui Ying Gao.  Generation of asparagine-linked glycan structure databases and their use , 2009, Journal of the American Society for Mass Spectrometry.

[149]  G. A. Jeffrey,et al.  Crystallographic studies of carbohydrates. , 1990, Acta crystallographica. Section B, Structural science.

[150]  Alessandro Laio,et al.  The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases. , 2007, Journal of the American Chemical Society.

[151]  G. Wiederschain,et al.  Essentials of glycobiology , 2009, Biochemistry (Moscow).

[152]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[153]  Peng George Wang,et al.  Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex Using AMBER and AUTODOCK , 2009, J. Chem. Inf. Model..

[154]  M. Betenbaugh,et al.  A mathematical model of N-linked glycosylation. , 2005, Biotechnology and bioengineering.

[155]  Young Joo Kim,et al.  Bioinformatics in the post-genome era. , 2004, Journal of biochemistry and molecular biology.

[156]  M. Vincent,et al.  Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method. , 2009, Physical chemistry chemical physics : PCCP.

[157]  Serge Pérez,et al.  Prospects for glycoinformatics. , 2005, Current opinion in structural biology.

[158]  J. J. Reina,et al.  Docking, synthesis, and NMR studies of mannosyl trisaccharide ligands for DC-SIGN lectin. , 2008, Organic & biomolecular chemistry.

[159]  Thomas Lütteke,et al.  Data mining the PDB for glyco-related data. , 2009, Methods in molecular biology.

[160]  C. Vicent,et al.  Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: NMR analysis of the structure and dynamics of aminoglycosides of the neomycin family. , 2002, Chemistry.

[161]  László Drahos,et al.  GlycoMiner: a new software tool to elucidate glycopeptide composition. , 2008, Rapid communications in mass spectrometry : RCM.

[162]  K. Julenius.  NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. , 2007, Glycobiology.

[163]  Martin Frank,et al.  Carbohydrate Structure Databases , 2010 .

[164]  Claus-Wilhelm von der Lieth,et al.  A (critical) survey of modelling protocols used to explore the conformational space of oligosaccharides , 1997 .

[165]  P. Nieto,et al.  NMR structural studies of oligosaccharides related to cancer processes. , 2008, Anti-cancer agents in medicinal chemistry.

[166]  Navnit Kumar Mishra,et al.  Molecular dynamics study of Pseudomonas aeruginosa lectin‐II complexed with monosaccharides , 2008, Proteins.

[167]  Andreas Bohne,et al.  SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides , 1999, Bioinform..

[168]  J. Marth,et al.  Glycosylation in Cellular Mechanisms of Health and Disease , 2006, Cell.

[169]  Vasant Honavar,et al.  Glycosylation site prediction using ensembles of Support Vector Machine classifiers , 2007, BMC Bioinformatics.

[170]  Catherine A. Cooper,et al.  GlycoMod – A software tool for determining glycosylation compositions from mass spectrometric data , 2001, Proteomics.

[171]  Alessio Ceroni,et al.  Software tool for the structural determination of glycosaminoglycans by mass spectrometry. , 2008, Analytical chemistry.

[172]  Robert J. Woods,et al.  NMR Spectroscopy and Computer Modeling of Carbohydrates: Recent Advances , 2006 .

[173]  René Ranzinger,et al.  Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans , 2008, BMC Structural Biology.

[174]  T. H. Thanka Christlet,et al.  Database analysis of O-glycosylation sites in proteins. , 2001, Biophysical journal.

[175]  Peng Liu,et al.  Inclusion mechanism of steroid drugs into beta-cyclodextrins. Insights from free energy calculations. , 2009, The journal of physical chemistry. B.

[176]  Edward Suh,et al.  A motif-based analysis of glycan array data to determine the specificities of glycan-binding proteins. , 2010, Glycobiology.

[177]  James Paulson,et al.  Automatic annotation of matrix‐assisted laser desorption/ionization N‐glycan spectra , 2005, Proteomics.

[178]  N. Hashii,et al.  The significance of glycosylation analysis in development of biopharmaceuticals. , 2009, Biological & pharmaceutical bulletin.

[179]  Tatsuya Akutsu,et al.  KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains , 2004, Nucleic Acids Res..

[180]  René Ranzinger,et al.  “Glyco‐peakfinder” – de novo composition analysis of glycoconjugates , 2007, Proteomics.

[181]  J. Abrahams,et al.  Characterization of a diagnostic Fab fragment binding trimeric Lewis X , 2009, Proteins.

[182]  Miroslava Cuperlovic-Culf,et al.  Carbohydrate microarrays: survey of fabrication techniques. , 2006, Omics : a journal of integrative biology.

[183]  Roland Stenutz,et al.  Web resources for the carbohydrate chemist. , 2004, Carbohydrate research.

[184]  Osamu Takahashi,et al.  The origin of the generalized anomeric effect: possibility of CH/n and CH/pi hydrogen bonds. , 2009, Carbohydrate research.

[185]  Peter J. Reilly,et al.  A Gibbs free energy correlation for automated docking of carbohydrates , 2008, J. Comput. Chem..

[186]  R. Field,et al.  Emerging glycomics technologies. , 2007, Nature chemical biology.

[187]  Seunho Jung,et al.  Retardation of the unfolding process by single N‐glycosylation of ribonuclease A based on molecular dynamics simulations , 2008, Biopolymers.

[188]  Pauline M Rudd,et al.  The impact of glycosylation on the biological function and structure of human immunoglobulins. , 2007, Annual review of immunology.

[189]  K Bock,et al.  The Complex Carbohydrate Structure Database. , 1989, Trends in biochemical sciences.

[190]  M. Frank.  Predicting Carbohydrate 3D Structures Using Theoretical Methods , 2009 .

[191]  Lara K Mahal,et al.  A ratiometric lectin microarray approach to analysis of the dynamic mammalian glycome , 2007, Proceedings of the National Academy of Sciences.

[192]  M. Berger,et al.  Identification and characterization of riproximin, a new type II ribosome‐inactivating protein with antineoplastic activity from Ximenia americana , 2006, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[193]  Chi-Huey Wong,et al.  Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[194]  H. Narimatsu,et al.  Bioinformatics for comprehensive finding and analysis of glycosyltransferases. , 2006, Biochimica et biophysica acta.

[195]  G. Boons,et al.  Comprehensive glycoscience : from chemistry to systems biology , 2007 .

[196]  Ajay K. Royyuru,et al.  Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity , 2009, J. Comput. Chem..

[197]  R. Dwek,et al.  Glycobiology , 2018, Biochimie.

[198]  S. Asher,et al.  Critical role of the solvent environment in galectin-1 binding to the disaccharide lactose. , 2009, Biochemistry.

[199]  Tim J. Stevens,et al.  A nomenclature and data model to describe NMR experiments , 2006, Journal of biomolecular NMR.

[200]  Hiren J. Joshi,et al.  GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update , 2003, Nucleic Acids Res..

[201]  R. Jefferis,et al.  Recombinant antibody therapeutics: the impact of glycosylation on mechanisms of action. , 2009, Trends in pharmacological sciences.

[202]  L. Wyns,et al.  2.06 – X-Ray Crystallography of Lectins , 2007 .

[203]  Naoyuki Taniguchi,et al.  Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. , 2007, Glycobiology.

[204]  C. Lieth.  2.10 – Databases and Informatics for Glycobiology and Glycomics , 2007 .

[205]  Karl Nicholas Kirschner,et al.  GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..

[206]  M. Akke,et al.  Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3 , 2009, Journal of biomolecular NMR.

[207]  Dirk Neumann,et al.  BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking , 2008, J. Chem. Inf. Model..

[208]  R. Service,et al.  Cinderella's Coach Is Ready , 2001, Science.

[209]  David Ozonoff,et al.  Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble , 2008, Chemical biology & drug design.

[210]  Per Erik Jansson,et al.  CASPER: a computer program used for structural analysis of carbohydrates , 1991, J. Chem. Inf. Comput. Sci..

[211]  Mark von Itzstein,et al.  Anti-influenza drugs: the development of sialidase inhibitors. , 2009, Handbook of experimental pharmacology.

[212]  M. DeMarco,et al.  Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces. , 2008, Glycobiology.

[213]  Junchao Xia,et al.  A tool for the prediction of structures of complex sugars , 2008, Journal of biomolecular NMR.

[214]  C. W. von der Lieth,et al.  LINUCS: linear notation for unique description of carbohydrate sequences. , 2001, Carbohydrate research.

[215]  Niklaus Fankhauser,et al.  Identification of GPI anchor attachment signals by a Kohonen self-organizing map , 2005, Bioinform..

[216]  David Goldberg,et al.  Automatic determination of O-glycan structure from fragmentation spectra. , 2006, Journal of proteome research.

[217]  Oliver Kohlbacher,et al.  TOPPView: an open-source viewer for mass spectrometry data. , 2009, Journal of proteome research.

[218]  Ken A Dill,et al.  Modeling water, the hydrophobic effect, and ion solvation. , 2005, Annual review of biophysics and biomolecular structure.

[219]  C. Lieth,et al.  GlycoCT-a unifying sequence format for carbohydrates. , 2008, Carbohydrate research.

[220]  A. Varki.  Sialic acids in human health and disease. , 2008, Trends in molecular medicine.

[221]  P. Jansson,et al.  Sequence determination of oligosaccharides and regular polysaccharides using NMR spectroscopy and a novel Web-based version of the computer program CASPER. , 2006, Carbohydrate research.

[222]  C. W. von der Lieth,et al.  The protein data bank (PDB) as a versatile resource for glycobiology and glycomics , 2006 .

[223]  Claus-Wilhelm von der Lieth,et al.  GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates , 2004, Nucleic Acids Res..

[224]  A. Laio,et al.  Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .

[225]  A. Imberty,et al.  Comparison of docking methods for carbohydrate binding in calcium-dependent lectins and prediction of the carbohydrate binding mode to sea cucumber lectin CEL-III , 2008 .

[226]  P. Albersheim,et al.  Letter to the Glyco-Forum CarbBank , 1992 .

[227]  B. Haab,et al.  Microarrays in glycoproteomics research. , 2009, Clinics in laboratory medicine.

[228]  P. Jedlovszky,et al.  GM1 ganglioside embedded in a hydrated DOPC membrane: a molecular dynamics simulation study. , 2009, The journal of physical chemistry. B.

[229]  Martin Frank,et al.  GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. , 2006, Glycobiology.

[230]  Knut Reinert,et al.  OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.

[231]  Pauline M Rudd,et al.  The conformational properties of the Glc3Man unit suggest conformational biasing within the chaperone-assisted glycoprotein folding pathway. , 2009, Journal of molecular biology.

[232]  M. Frank.  Conformational Analysis of Carbohydrates – A Historical Overview , 2009 .

[233]  Rolf Apweiler,et al.  Bioinformatics database infrastructure for biotechnology research. , 2006, Journal of biotechnology.

[234]  F. J. Krambeck,et al.  A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data. , 2009, Glycobiology.

[235]  A. Varki,et al.  Overview of Glycoconjugate Analysis , 2009, Current protocols in protein science.

[236]  Toshihide Shikanai,et al.  The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures , 2005, Bioinform..

[237]  Jun Hirabayashi,et al.  Concept, strategy and realization of lectin-based glycan profiling. , 2008, Journal of biochemistry.

[238]  Claus-W von der Lieth,et al.  GLYCO‐FRAGMENT: A web tool to support the interpretation of mass spectra of complex carbohydrates , 2003, Proteomics.

[239]  Tatsuya Akutsu,et al.  A score matrix to reveal the hidden links in glycans , 2005, Bioinform..

[240]  Hiroshi Mamitsuka,et al.  Informatic innovations in glycobiology: relevance to drug discovery. , 2008, Drug discovery today.

[241]  Christophe Meynier,et al.  Computational Studies of Human Galectin-1: Role of Conserved Tryptophan Residue in Stacking Interaction with Carbohydrate Ligands , 2009, Journal of biomolecular structure & dynamics.

[242]  B. Ramakrishnan,et al.  2.07 – X-Ray Crystal Structures of Glycosyltransferases , 2007 .

[243]  Jaroslav Koca,et al.  Structures and mechanisms of glycosyltransferases. , 2006, Glycobiology.

[244]  J. Ståhlberg,et al.  X‐ray crystal structures of Phanerochaete chrysosporium Laminarinase 16A in complex with products from lichenin and laminarin hydrolysis , 2009, The FEBS journal.

[245]  Hiroshi Yasuda,et al.  A gram distribution kernel applied to glycan classification and motif extraction. , 2006, Genome informatics. International Conference on Genome Informatics.

[246]  J. Vliegenthart,et al.  Analysis of glycoprotein-derived glycopeptides. , 2000, EXS.

[247]  Daniel L. Rubin,et al.  Biomedical ontologies: a functional perspective , 2007, Briefings Bioinform..

[248]  Don C. Wiley,et al.  Structure of an unliganded simian immunodeficiency virus gp120 core , 2005, Nature.

[249]  S. Withers,et al.  Elucidating the nature of the Streptomyces plicatus beta-hexosaminidase-bound intermediate using ab initio molecular dynamics simulations. , 2008, Journal of the American Chemical Society.

[250]  Søren Brunak,et al.  O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins , 1999, Nucleic Acids Res..

[251]  Marcelo A Martí,et al.  Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy. , 2009, The journal of physical chemistry. B.

[252]  D. Kilpatrick.  Handbook of animal lectins : properties and biomedical applications : a compendium of galectins, collectins, selectins, pentraxins and other carbohydrate-binding proteins from throughout the animal kingdom , 2000 .

[253]  P. Seeberger,et al.  Carbohydrate arrays as tools for research and diagnostics. , 2008, Chemical Society reviews.

[254]  P. Kersey,et al.  In Silico Characterization of Proteins: UniProt, InterPro and Integr8 , 2008, Molecular biotechnology.

[255]  Søren Brunak,et al.  Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function , 2001, Pacific Symposium on Biocomputing.

[256]  Wei Lang,et al.  Advancing glycomics: implementation strategies at the consortium for functional glycomics. , 2006, Glycobiology.

[257]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[258]  Pekka Mark,et al.  Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo‐transglycosylases and endo‐hydrolases , 2009, Proteins.

[259]  Robert J Woods,et al.  Structural glycobiology: A game of snakes and ladders , 2008, Glycobiology.

[260]  Kiyoko F. Aoki-Kinoshita.  An Introduction to Bioinformatics for Glycomics Research , 2008, PLoS Comput. Biol..

[261]  Roger A. Laine,et al.  Invited Commentary: A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems , 1994 .