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Showing 20 records out of 380 total
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Categories: proteomics, (protein sequences and identification, proteomics experiment, function analysis) - Software type(s): website - tool
Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The program scans a protein sequence against the PRINTS Protein Fingerprint Database.
Categories: proteomics, (protein structure) - Software type(s): website - tool
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors
Categories: proteomics, (protein structure) - Software type(s): website - tool
Geno3D is an automatic web server for protein molecular modelling
Categories: systems biology - Software type(s): CLI, GUI - tool
A tool to extract duplicate genes and their amino acid and synonymous divergence from completely sequenced genomes.
keywords:
Categories: systems biology, evolutionary biology - Software type(s): website - tool
A genotype network is a graph in which vertices represent genotypes that have the same phenotype. The Genonets Server is a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography; (iii) multiple interactive visualizations.
keywords: network
Categories: proteomics, (protein structure) - Software type(s): website - tool
GlobPlot is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder
Categories: glycomics - Software type(s): website - tool
The tools at GLYCAM-Web automate the prediction of 3D structures of glycans, glycosaminoglycans, and glycoproteins, and provide all files necessary for the user to perform molecular dynamics simulations of these systems with the AMBER software package. Additional tools facilitate the prediction of the specificity of glycan binding proteins, such as lectins and antibodies, and provide theoretical 3D structures for these complexes.
Categories: glycomics - Software type(s): website - tool
Exoglycosidase cleavage of monosaccharides results in signature peak shifts, in both UPLC and MS1. Manual interpretation of exoglycosidase data is complex and time consuming. GlycanAnalyzer is a web application that pattern matches N-glycan peak shifts following exoglycosidase digestion and automates structure assignments. GlycanAnalyzer significantly improves assignment accuracy over other auto-assignment methods on tests with a monoclonal antibody.
Categories: glycomics - Software type(s): website - tool
Calculate the mass of an oligosaccharide structure.
Categories: glycomics - Software type(s): website - database
A single entry portal to access three-dimensional features of (1) carbohydrate and carbohydrate polymers in different physical and biological conditions, a nd (2) carbohydrate-binding proteins crystallised with their carbohydrate ligands (lectins, monoclonal antibodies, glycosyltransferases). Most data is structural data arising from diffraction experiments, but three-dimensional models resulting from theoretical calculations are also included. 3D structures can be viewed across the website.
Categories: glycomics - Software type(s): website - tool
GlycoDigest is a tool that simulates the action of these exoglycosidases on released oligosaccharides. It assists glycobiologists in designing enzyme mixtures that can be used to guide the precise determination of glycan structures.
Categories: proteomics, glycomics - Software type(s): website - tool
The GlycoDomain Viewer is a tool for the visualisation of glycosylation sites in the context of the protein and conserved domains. It contains O-glycoproteomic data from the Clausen lab, and predictions of GalNAc-type glycosylation for the human proteome.
Categories: proteomics, (protein sequences and identification, proteomics experiment, protein modifications), glycomics - Software type(s): website - tool
Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
Categories: proteomics, glycomics - Software type(s): website - database/tool
GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carries them, the enzymes that synthesise or degrade them and the proteins that bind them. GlyConnect also integrates tools otherwise accessible individually in the glycomics collection of ExPASy.
Categories: glycomics - Software type(s): website - tool
Compozitor queries the GlyConnect database to bring out contextual information relative to a set of glycan compositions (glycome). The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database.
Categories: glycomics - Software type(s): website - database
GlycoPedia collects e-chapters on basic, intermediary and advanced topics of glycoscience. It also compiles various sources and suggests relevant readings to the scientific community.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
GlycoSiteAlign selectively aligns amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.
Categories: glycomics - Software type(s): website - tool
GlyCosmos is a Web portal for omics data pertaining to the glycosciences. Based on Semantic Web technologies, data in Resource Description Framework (RDF) are stored in a publicly available SPARQL endpoint, and user interfaces are provided to easily browse and search this data. Repositories pertaining to glycans (GlyTouCan), glycomics data (GlycoPOST) and glycoconjugates (GlyComb) are available, as well as entry points for genes, proteins, lipids, pathways, diseases and glycomes.
keywords: glycomics
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