Services: proteins and proteomes

A reusable platform-independent API call component for protein metadata alignment, annotation, and integration across major protein data resources.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

An integrative platform for the analysis of transcriptomics, proteomics and genomic data

with advanced functional profiling.

Predicts the subcellular localization of proteins in eukaryotes.

Either as a cooperation or consultancy service.

A web server integrating multiple tools for prediction of protein subcellular localization and topological features

General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

A classification of protein structures and sequences that groups protein domains into superfamilies. 

An R package used for efficient unraveling of the inherent dynamic properties of pathways.

COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.

System for identification of alterations using protein mass spectrometry.

Prediction of secretory signal peptides and cleavage sites in proteins.

We provide support and guidance in development of Disease Maps (disease-maps.org), computational and visual repositories of knowledge about mechanisms of human diseases. We offer hosting of open access Disease Maps on the MINERVA Platform (minerva-web.lcsb.uni.lu) on our infrastructure under the elixir-luxembourg.org sub-domain, their backup and conservation. The MINERVA Platform ensures online access, interactive exploration, search for known drug targets and visualisation of omics datasets. We provide training in management of the Disease Maps and guidance to their integration into reproducible computational workflows by using the dedicated API of the hosting platform.

A manually curated community resource annotating proteins for experimentally determined regions of intrinsic disorder from the literature.

This resource includes sequence pipeline (TarO) analysis, a secondary prediction (JPred) structure server, and a protein kinase database and kinase classification pipeline (Kinomer).

Tool to predict backbone dynamics from a single protein sequence

Efficient detection of protein disorder: web server and tool for protein region detection which are thought to contain no structural content.

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

A database of functionally important residues from proteins of known structure.

FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. Proteins find their use in numerous biomedical and biotechnological applications. Naturally occurring proteins usually cannot withstand harsh industrial environments since they have evolved to function under mild conditions. Increasing protein stability is one of the key determinants of protein applicability. The predictive power of the current computational tools is compromised by the limited experimental data that would allow a rigorous training and testing.

A server for predicting catalytic and ligand-binding residues in protein sequences.

An integrated platform for macromolecular flexibility studies.

Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

A database of structural features for three galactose metabolism enzymes (GALT, GALK, GALE).

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.

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 carry them, the enzymes that synthesise or degrade them and the proteins that bind them.

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases.