Table 2.
Web-based tools for computational studies of GAGs. Accession date for all the links reported in the table: 12 April 2021. FF: force field.
| Name | Description (Website) | Ref. |
|---|---|---|
| Databases | ||
| PDB | Bio-macromolecular structures. (http://www.rcsb.org/pdb/) | [51] |
| PubChem | Open chemical database containing the structures of small and large molecules including GAGs with their respective annotations (chemical structures, identifiers, physical properties, biological activities, patents, safety and toxicity data). (https://pubchem.ncbi.nlm.nih.gov) | [52] |
| KEGG GLYCAN |
Collection of experimental GAG structures taken from CarbBank or from recent publications and present in KEGG pathways. (https://www.genome.jp/kegg/glycan/) | [53] |
| Zinc | Curated collection of commercially available chemical compounds in ready-to-dock, 3D formats. (https://zinc.docking.org) | [54] |
| DrugBank | Detailed drug properties (chemical, pharmacological and pharmaceutical features) and target information (sequences, structures and pathway). (https://go.drugbank.com) | [55] |
| EMBL-EBI | Collection of various tools and data from different sources (including those listed in this table) (https://www.ebi.ac.uk) | [56] |
| GAG-database | Comprehensive resource for 3D-structures of GAGs, oligosaccharides and their complexes with proteins (140 curated entries). (https://www.gagdb.glycopedia.eu) | [57] |
| monosaccharides database | Comprehensive resource for monosaccharides. (776 entries). (http://monosaccharidedb.org) | [58] |
| Tools to Build a GAG | ||
| CarbBuilder | Builds GAG 3D-structures with CHARMM FF from pre-calculated glycosidic linkage torsions. (https://people.cs.uct.ac.za/~mkuttel/Downloads.html) | [59] |
| Chemsketch | Converts 2D drawings into 3D structures using a modified molecular mechanics approach. (https://www.acdlabs.com/resources/freware/chemsketch/) | [60] |
| GLYCAM-Web GAG Builder | Models GAG 3D-structures with GLYCAM06 FF using the AMBER MD package in an automated system. (http://glycam.org/gag) | [61] |
| CHARM-GUI Glycan Modeller | In silico N-/O-glycosylation of proteins; modeling of GAG-only systems. (http://www.charmm-gui.org/?doc=input/glycan) | [62] |
| Amber-tleap | Models GAG 3D-structures with the GLYCAM06 FF using the AMBER MD package. (https://ambermd.org) | [63] |
| MOE | Models GAG 3D-structures with MMFF94, AMBER, CHARMM FF and semi-empirical energy functions (PM3, AM1, MNDO). Conformational analysis using either a systematic or a stochastic search using random rotation of bonds. (https://www.chemcomp.com/MOE-Molecular_Modeling_and_Simulations.htm) | [64] |
| PRODRG | Models GAG 3D-structures with the ffgmx GROMACS FF. (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg) | [65] |
| Macromodel | Models GAG 3D-structures with MM2, MM3, AMBER, AMBER94, MMFF, MMFFs, OPLS, OPLS_2005 and OPLS3 FF. (https://www.schrodinger.com/products/macromodel) | [66] |
| Software for Molecular Docking | ||
| Autodock | Stochastic local search and Lamarck genetic algorithm and empirical scoring function. (http://autodock.scripps.edu/) | [67] |
| Autodock-Vina | Gradient-based local search, iterated local search algorithm and empirical scoring function. (http://vina.scripps.edu/index.html) | [68] |
| Glide | Search algorithms include the modes of extra precision, standard precision and a high-throughput virtual filter. (https://www.schrodinger.com/products/glide) | [69] |
| Dock | Step-by-step geometric matching strategy; AMBER FF, empirical scoring function. (http://dock.compbio.ucsf.edu) | [70] |
| Gold | Genetic algorithm. (https://www.ccdc.cam.ac.uk/solution/csd-discovery/components/gold/) | [71] |
| HADDOCK | Encodes information from identified or predicted interfaces in ambiguous interaction restraints. (https://wenmr.science.uu.nl/haddock2.4/library) | [72] |
| ClusPro | Fast Fourier Transform-based algorithm and molecular mechanics energy function for scoring. (https://cluspro.bu.edu/login.php) | [73] |
| VinaCarb | Carbohydrate intrinsic-energy functions implemented in AutoDock Vina software. (http://glycam.org/docs/othertoolsservice/download-docs/publication-materials/vina-carb/) | [74] |
| GlycoTorc-Vina | Based on the VinaCarb program; uses QM-derived scoring functions to improve GAGs docking. (http://ericboittier.pythonanywhere.com/) | [75] |
| GAG-dock | Modification of DarwinDock method for sulfated GAGs. | [76] |
| FFs for GAGs | ||
| GLYCAM_06 | Set of parameters and quantum mechanical data for a collection of minimal molecular fragments and related small molecules for GAGs simulation. (http://glycam.org/docs/forcefield/) | [77] |
| CHARMM FF for carbohydrates | Hierarchical parametrization of model compounds containing the key atoms in GAGs. (http://www.charmm.org/charmm/resources/charm-force-fields/#charmm) | [78] |
| GROMOS 53A6glyc | Refined potential parameters for the determination of hexopyranose ring conformations by fitting to the corresponding quantum-mechanical profiles. (https://www.biomatsite.net/software) | [79] |