Representations

REPRESENTATIONS

NOMENCLATURE

• IUPAC www.sbcs.qmul.ac.uk/iupac/2carb/ Carbohydrate Nomenclature
• SNFG https://www.ncbi.nlm.nih.gov/glycans/snfg.html, Symbol Nomenclature for Glycans
• GlycoCT GlycoCT-a unifying sequence format for carbohydrates.
• WURCS* WURCS : the Web3 Unique Representation of Carbohydrate Structures.
• KCF Format used in the KEGG database
• LINUCS www.glycosciences.de/modeling/sweet-remote/ Linear Notation for Unique Description of Carbohydrate Structures
• Glyde II GLYDE-II : The GLYcan Data Exchange format
• PubChem Sketcher https://pubchem.ncbi.nlm.nih.gov/edit2/ From drawn structures generates SMILES, SMARTS, InChI and InChIKey

CONVERSION : Utilities

• GlycoCT = WURCS https://glytoucan.org/Structures/structureSearch
• Convert Tool convert from any format (GlycoCT condensed, KCF, IUPAC, LinearCode, LINUCS) to (almost) any other format (depending on input)
  http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/convert/index.pl
• GlycoCTcondensed to KCF : convert a glycan structure in GlycoCT format to KCF http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/GlycoCTtoKCF_au/glycoct_index_au.pl
• GlycoCTXML to KCF : convert a glycan structure in GlycoCT format to KCF
  http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/GlycoCTtoKCF/glycoct_index.pl
• GlycoCT to CSDB Linear : http://csdb.glycoscience.ru/database/core/translate.html
• GLYDE2 to KCF : convert a glycan structure in GLYDE2 to KCF
  http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/GLYDE2toKCF/glyde2_index.pl
• IUPAC to KCF : convert a glycan structure in IUPAC format to KCF
  http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/IUPACtoKCF_au/iupactokcf_index_au.pl
• LINUCS to KCF convert a glycan structure in LINUCS format to KCF http://rings.t.soka.ac.jp/cgi-bin/tools/utilities/LINUCStoKCF/linucs_to_kcf_index.pl
• CSDB Linear to GlycoCT, Glyde-II, LinUCS, WURCS, GLYCAM, SMILES, 3D MOL http://csdb.glycoscience.ru/database/core/translate.html#from
• CSDB Linear to SweetDB, SNFG, structural formula image http://csdb.glycoscience.ru/database/core/check_structures.html

COMPOSITION

• GlycanMass https://web.expasy.org/glycanmass/ GlycanMass is a tool which allows calculating the mass of an oligosaccharide structure
• SwissMassAbaccus https://glycoproteome.expasy.org/swiss-mass-abacus/ Swiss Mass Abacus is a calculator of peptide and glycopeptide masses.

DRAWING

• GlycanSketcher https://glycoproteome.expasy.org/sugarsketcher/
  https://github.com/alodavide/sugarSketcher, SugarSketcher : Quick and Intuitive Online Glycan Drawing
• Glycan Builder http://sugarbind.expasy.org/builder An interface for building and displaying glycan structures
• Draw Glycan SNFG http://www.virtualglycome.org/DrawGlycan/ The symbol nomenclature for glycans (SNFG) contains 67 different monosaccharides represented using various colors and geometric shapes.
• DrawRingS http;//www.rings.t.soka.ac.jp/DrawRINGS: 2D HTML5-based glycan structure drawing tool for generating KCF and IUPAC format and/or querying the RINGS database, ...
• LiGraph : generates schematic drawings of oligosaccharides which are often used to display glycan structure.

3D-ANALYSERS

• Carp http://www.glycosciences.de/tools/carp/
  generates Ramachandran-like plots of carbohydrate linkage torsions in pdb-files.
• Azahar a PYMOL plugin for construction, visualization and analysis
• pdb-carewww.glycosciences.de/tools/pdb-care/ checks carbohydrate residues in pdb-files for errors.
• pdb2linucs www.glycosciences.de/tools/pdb2linucs/
  automatically extracts carbohydrate information from pdb-files and displays it using the LINUCS-Code

3D-BUILDERS

• doGlycans Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.
• Glycan-Web Carbohydrate, Glycoprotein, GAGs Builder
• Sweet Sweet is a program for constructing 3D models of saccharides from their sequences using standard nomenclature
• PolysGlycanBuilder Algal, Bacterial, GAG, Plant Polysaccharides, N-O linked Glycan
• CHARMM Gui http://www.charmm-gui.org/?doc=input/glycan An option within the Glycan Reader & Modeler section of the general menu
• Carbuilder https://people.cs.uct.ac.za/~mkuttel/CBresidues.html
• Rosetta Carbohydrate https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans
• Others Several Molecular Modeling software have provision to build 3D structures of glycan

3D-VIEWERS

• LiteMol Powerful and blazing-fast tools for handling 3D macromolecular data in the browser
• Glycan-Web 3D-Symbol Nomenclature for Glycans
• SweetUnityMol : Molecular 3D structures (SNFG compliant) and networks viewer . Virtual Reality. Manual
• Glycan-Web 3D-Symbol Nomenclature for Glycans
• Others Several Molecular Viewer platforms have provision to display 3D structures of glycan