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 MOLhttp://csdb.glycoscience.ru/database/core/translate.html#from
- CSDB Linear to SweetDB, SNFG, structural formula imagehttp://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 Carbohydratehttps://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