Table 2.
Informatics tools for carbohydrate and glycoprotein modeling, 3D structure prediction and analysis.
| Tool | Description | Type a | Reference |
|---|---|---|---|
| Structure modeling | |||
| CHARMM-GUI Glycan Modeler | In silico N-/O-glycosylation of proteins;modeling of carbohydrate-only systems | Web-service | [230] (http://www.charmm-gui.org/?doc=input/glycan) |
| CHARMM-GUI Glycolipid/LPS Modeler | Glycolipid and lipoglycan structure modeling | Web-service | [230] (http://charmm-gui.org/?doc=input/glycolipid) (http://charmm-gui.org/?doc=input/lps) |
| Glycosylator | Rapid modeling of glycans and glycoproteins (including glycosylation) based on CHARMM force field | Python framework | [231] (https://github.com/tlemmin/glycosylator) |
| RosettaCarbohydrate | Modeling a wide variety of saccharide and glycoconjugate structures (including loop modeling, glyco-ligand docking and glycosylation) | Python framework | [228,232,233,234] (https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans) |
| Azahar | Monte Carlo conformational search and trajectory analysis of glycans | Python framework; PyMol plugin | [235] (https://github.com/BIOS-IMASL/Azahar) |
| Shape | Carbohydrate-dedicated fully automated MM3-based conformation simulation | Standalone software | [236] (https://sourceforge.net/projects/shapega/) |
| Glydict | MM3-based N-glycan structure prediction based on MD simulations | Web-service | [237] (http://www.glycosciences.de/modeling/glydict/) |
| GLYGAL | MM3-based conformational analysis of oligosaccharides | Standalone software | [238] |
| Fast Sugar Structure Prediction Software (FSPS) | Automatic structure prediction tool for oligo- and polysaccharides in solution | Standalone software | [239,240,241,242] |
| Glycosylation modeling and grafting | |||
| GLYCAM-Web Glycoprotein Builder | Attaching a glycan (user input) to a protein (PDB file) | Web-service | (http://glycam.org/gp) |
| GlyProt | In silico generation of N-glycosylated 3D models of proteins | Web-service | [243] (http://www.glycosciences.de/modeling/glyprot/php/main.php) |
| Phenix CarboLoad | Loading a carbohydrate structure into protein model and PDB file generation | Python framework | [244] (https://www.phenix-online.org/documentation/reference/carbo_load.html) |
| GLYCAM-Web GlySpec (Grafting) | Prediction of glycan specificity by integrating glycan array screening data and 3D structure | Web-service | [245,246,247,248,249] (http://glycam.org/djdev/grafting/) |
| Biological membranes and micelles | |||
| CHARMM-GUI Membrane Builder | Building complex glycolipid-/LPS-/LOS-containing biological membrane systems | Web-service | [230,250,251,252,253] (http://www.charmm-gui.org/?doc=input/membrane.bilayer) |
| GNOMM (gram-negative outer membrane modeler) | Automated building of lipopolysaccharide-rich bacterial outer membranes (3D model preparation for MD simulations in GROMACS) | Standalone software | [254] (http://thalis.biol.uoa.gr/GNOMM/) |
| Micelle Maker | Micelle building based on broad range of starting lipids and glycolipids (3D model preparation using AMBER software package and GLYCAM library) | Web-service | [255] (http://micelle.icm.uu.se/) |
| Carbohydrate moiety identification | |||
| Cheminformatics Tool for Probabilistic Identification of Carbohydrates (CTPIC) | Identification of small saccharides and their derivatives (input in SDF or MOL format) | Web-service | [256] (http://ctpic.nmrfam.wisc.edu/) (https://github.com/htdashti/ctpic) |
| Sails | Automated identification of linked sugars | Python framework | (https://github.com/glycojones/sails) |
| GlyFinder | Locating relevant carbohydrate-containing structures in Protein Data Bank | Part of web-service pipeline | [257,258] (https://dev.glycam.org/portal/gf_home/) |
| pdb2linucs | Extraction of carbohydrate data from a PDB file | Web-tool | [259] (http://www.glycosciences.de/tools/pdb2linucs/) |
| GLYCAM-Web PDB-preprocessor | Processing of PDB files with (glyco-)proteins for AMBER-style output | Web-service | (http://glycam.org/pdb) |
| Sugar identification program | Identifying the residue names of carbohydrates in a PDB file | Standalone software | (http://glycam.org/docs/othertoolsservice/downloads/downloads-software/) |
| Glycan Reader | Automated sugar identification and simulation preparation for carbohydrates and glycoproteins in PDB files | Web-service | [260,261] (http://glycanstructure.org/glycanreader/) (http://www.charmm-gui.org/?doc=input/glycan) |
| Structure building and model preparation | |||
| doGlycans | Preparing carbohydrate structures (including polysaccharides, glycolipids and glycoproteins) for GROMACS atomistic simulations | Python framework | [262] (https://bitbucket.org/biophys-uh/doglycans/src/master/) |
| GLYCAM-Web Carbohydrate builder | 3D structure prediction of carbohydrates and related macromolecules using GLYCAM06 force field and MD in AMBER (successor of GLYCAM Biomolecule Builder (http://glycam.org/old/biombuilder/biomb_index.jsp)) | Web-service | [177] (http://glycam.org/) |
| SWEET-II | Rapid 3D model construction of oligo- and polysaccharides with MM3 optimization | Web-service | [263,264] (http://www.glycosciences.de/modeling/sweet2/) |
| REStLESS API | 3D structure generation of carbohydrates and derivatives from CSDB Linear notation with MMFF94 optimization (including aglycone moiety) | Web-service | [265] (http://csdb.glycoscience.ru/database/core/translate.html#from) |
| Polysaccharide builders | |||
| POLYS | 3D structure generation of poly- and complex oligosaccharides from MM2-precalculated glycosidic linkage torsions and energy minimization | Web-service | [266,267] (https://bitbucket.org/polys/polys/src/default/) (http://glycan-builder.cermav.cnrs.fr/) |
| CarbBuilder | Building of 3D structures of polysaccharides in CHARMM force field from pre-calculated glycosidic linkage torsions | Standalone software | [268,269] (https://people.cs.uct.ac.za/~mkuttel/Downloads.html) |
| GAG-builder | Translating of GAG sequences into 3D models based on POLYS glycan builder | Web-service | [270] (http://glycan-builder.cermav.cnrs.fr/gag/) (http://matrixdb.univ-lyon1.fr/) |
| GLYCAM-Web GAG Builder | Modeling of GAG 3D structure in GLYCAM06 force field using AMBER MD package | Web-service | [271] (http://glycam.org/gag) |
| Docking | |||
| BALLDock/SLICK | Protein-carbohydrate complex docking software | Standalone software, a module in docking software | [272,273] (https://ball-project.org/download/) |
| HADDOCK | Modeling of biomolecular complexes with support of glycosylated proteins | Web-service | [274] (https://wenmr.science.uu.nl/haddock2.4/library) |
| Vina-Carb | CHI-energy functions implemented in AutoDock Vina software | Standalone software | [156,157] (http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/vina-carb/) |
| GLYCAM-Web Antibody docking | Docking of an antibody (from a PDB file) to a glycan antigen (from a library or user input) | Web- service | (http://glycam.org/ad) |
| Cluspro | Sulfated GAG docking (as one of options) | Web-service | [275,276] (https://cluspro.bu.edu/login.php) |
| GAGDock (DarwinDock) | Modification of DarwinDock method for sulfated glycosaminoglycans | Algorithm | [277] |
| GlycoTorch Vina | Docking of sulfated glycosaminoglycans based on Vina-Carb | Standalone software | [278] (http://ericboittier.pythonanywhere.com/) |
| Structural data analysis | |||
| Conformational Analysis Tool (CAT) | Analysis of carbohydrate molecular trajectory data derived from MD simulations | Standalone software | [279] (http://www.md-simulations.de/CAT/) |
| Best-fit, Four-Membered Plane (BFMP) | Analysis of conformational data from crystal structures and MD simulations of carbohydrates | Standalone software | [280] (http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/bfmp/) |
| Distance Mapping | Estimation of nuclear Overhauser effects in disaccharides | Web-tool | (http://www.glycosciences.de/modeling/distmap/) |
| MD2NOE | Calculation of Nuclear Overhauser effect build-up curves from long MD trajectories | Standalone software | [281] (http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/md2noe/) |
| GS-align | Glycan structure alignment and similarity calculation | Standalone software | [282] (http://www.glycanstructure.org/gsalign) |
| GlyTorsion | Analysis of torsion angles in carbohydrates from Protein Data Bank | Web-tool | [283] (http://www.glycosciences.de/tools/glytorsion/) |
| GlyVicinity | Analysis of amino acids in the vicinity of carbohydrate residues derived from Protein Data Bank | Web-tool | [284] (http://www.glycosciences.de/tools/glyvicinity/) |
a Web-service implies an automated pipeline for running a specific software (e.g., molecular modeling, structure building, carbohydrate coordinate extraction, format conversion). It results in 3D structural data output starting from primary structure input or atomic coordinate file upload. Web-tool is employed for 3D structural data processing and analysis without 3D structural data output; it is a simpler application designed primarily for statistics and visualization. Other types are self-explanatory.