Allows to query the database GlyTorsionDB. GlyTorsion performs a graphical output of results by generating diagrams or plots. GlyTorsionDB contains the torsion angle values of all carbohydrate linkages present in the PDB. This tool permits users to see which angles are preferred by the residues of interest.
Evaluates the quality of a protein 3D structure using protein backbone torsion angles. Carp permits users to query GlyTorsionDB, a database containing the torsion angle values of all carbohydrate linkages present in the Protein Data Bank (PDB). It is based on the pdb2linucs algorithm. This tool is able to generate separate plot for each different linkage type.
Offers the opportunity for open source development that integrates multiple web resources into reproducible workflows using Galaxy. The GAP’s integration of glycomics tools into an established bioinformatics web platform to improve their accessibility, usability, re-usability improves the sharing and reproducibility of computational analysis and data in glycomics. Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services.
Automates elucidation of regular poly- and oligomeric carbohydrate structures. GRASS employs a fast nuclear magnetic resonance (NMR) simulation method for rough ranking against the experimental NMR spectrum. It is based on an accurate simulation method for making refinement. This tool utilizes an incremental scheme with a steric correction parameterized for multiple carbohydrate and non-carbohydrate residues and bond types.
Assists in building applications that require seamless and secure communication over HTTP. Restless is a comprehensive and consistent programming model with the ability to simulate a range of business processes, designed to target mobile, tablet, desktop and embedded production environments. It also provides an automated programming interface (API) designed for unmanned processing by other glycoinfomatic projects.
Serves as a builder for polysaccharides and complex carbohydrates. POLYS’s main goal is to produce a molecular builder with sufficient versatility to handle the complexity of most if not all complex carbohydrates and carbohydrate polymers. This software benefits of features such as a builder syntax related to standard carbohydrate nomenclature and chosen conventions for data inputs to guarantee the fact that this tool can be utilized in a multitude of computing environments.
Designs O-glycan structures and permits the discovery of the wide variety of possible oligosaccharide structures formed by the activities of several known enzymes of O-glycosylation. O-Glycologue serves for testing the effects of knockouts of the enzymes of O-linked glycosylation on glycoform heterogeneity. It is useful to predict the biosynthetic pathways forming particular O-glycans.
Determines 3D structures of carbohydrates and macromolecular structures involving carbohydrates in a simplified manner. GLYCAM-Web permits users to study ring conformational interconversions. This tool is able to remove dependency on the AMBER force field and parameters. In addition, GLYCAM-Web uses a single dihedral angle term for each molecular-class-specific linkage.
Allows users to prepare carbohydrate structures. doGlycans tool set is composed of two features: (i) prepreader.py, for preparing the carbohydrate chains for polymer simulations and; (ii) doglycans.py that prepares models for glycoproteins and glycolipids. The toolkit creates topologies of carbohydrates in the GROMACS format and then provides 3D structures of carbohydrates covalently linked to the given lipids and proteins.
Serves for displaying and comparing glycan profiles. Glynsight enables the composition of glycans. It can bring out hidden patterns inside or among glycan profiles. This tool allows users to export each profile as an image or the whole collection in form of a JSON file. It offers potential glycan structures related to specific compositions. The software is able to perform simultaneous comparison of large collections of profiles.
Extends the PyMOL's capabilities to visualize, analyze and model glycans and glycoconjugated molecules. Azahar provides convenient functions to compute and visualize molecular properties useful to study glycans: the radius of gyration, Ramachandran plots and hydrogen bonds. Azahar contains to date 23 monosaccharide templates which are available to build glycan molecules trough the plugin’s graphical user interface (GUI).
Identifies and assigns carbohydrate structures using only the reported atom types and their 3D atom coordinates. pdb-care allows users to analyse a file obtained directly from PDB using the PDB-ID, or to provide a pdb-file located on the local computer. It is based on a carbohydrate detection software. This tool uses the LINUCS-notation to normalise complex carbohydrate structures.
Generates a complete structural description of the complete glycan, which can be easily transformed to the IUPAC nomenclature. Pdb2linucs is able to automatically extract carbohydrate information from PDB-files.
Converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. LINUCS can be applied on any molecules and to all types of carbohydrates.
A format based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.
Provides algorithmic and data mining tools to aid glycobiology research. RINGS is a freely available Web resource for glycobiologists to analyze their data using the latest data mining and algorithmic techniques. It provides a number of tools including a 2D glycan drawing and querying interface like DrawRINGS, a Glycan Pathway Predictor (GPP) tool for dynamically computing the N-glycan biosynthesis pathway from a given glycan structure, and data mining tools Glycan Miner Tool and Profile PSTMM. RINGS offers free access to these methods for academic research.
Allows statistical analyses on the types of amino acids around carbohydrate chains. GlyVicinity can also proceed analyses on atoms forming the closest contacts between protein and carbohydrate residues.
A computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing (MAGS), which combines mass spectrometry analyses with glycan structural information from glycan microarray technology. This approach to computational sequencing of the unknown glycans requires (a) determination of the glycan composition using MALDI-TOF analysis, (b) interrogation of the glycans with lectins and antibodies that bind known determinants, (c) determination of the set of predicted structures based on automated meta-analysis of the experimental data from the virtual glycome database given the constraints of the rules for the biosynthetic pathway of the glycans.
0 - 0 of 0