Services: Enzymes, Interactions And Pathways

The BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references.

A comprehensive enzyme information system. It is the world’s largest and most widely information system on all aspects of enzymes, including function, structure, mutants, properties like stability, purification. Data download is possible as an integrated text filed or via SOAP.

CellNetAnalyzer is a MATLAB toolbox for analyzing the structure and function of biological networks.

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes.

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

A server for calculating contact maps of X-ray, NMR and predicted structures.

OPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

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 bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.

ENZYME is a repository of information on enzyme nomenclature based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ENZYME describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

Online platform for comparing methylation data

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

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

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its qualitative dynamical behaviour.

GraphWeb is a public web server for graph-based analysis of biological networks.

Estimation of transmembrane regions based on amino acid sequence

IntAct provides a freely available, open source database system and analysis tools for molecular interaction data.

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

Access to aRNA research tools for secondary structure prediction, structure alignments, interaction prediction, kinetics etc. Databases and Utils include:

• TRNAdb
• Mitos
• DARIO
• Plexy
• RNAsnoop
• RNAstrand 
• Ryoto

Lipidomics Informatics for Life Sciences (LIFS) provides the bioinformatic framework to understand lipids in context and create an integrative systems biology view for lipid research.

MatrixDB is a database focused on molecular interactions of extracellular matrix proteins and glycosaminoglycans. The advanced query interface allows users to browse MatrixDB data, to build and to visualize specific interaction networks based on transcriptomic or quantitative proteomic data, diseases, biological processes or molecular functions. MatrixDB hosts the GAG builder tool to build on line 3D models of GAG sequences binding to proteins. 

A comprehensive collection of data from manually curated protein-protein interaction databases adhering to the IMEx consortium.

MetExplore is a free and open webserver for the analysis of omics data in the context of genome scale metabolic networks. MetExplore allows the collaborative curation of metabolic networks. In the specific case of metabolomics, it provides mining algorithms such as MetaboRank, a recommendation system for enhanced metabolic fingerprinting. Overall, Metexplore orginality relies in its ability to allow taylor made metabolic network visualisation using an open source javascript library: MetExploreViz.

MetFrag is a system for the annotation of tandem mass spectra of metabolites, performing in silico fragmentation and scoring.

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

The Molecular INTeraction Database of protein-protein interactions curated from peer-reviewed papers. An ELIXIR Core Data Resources and founder member of the IMEx Consortium.

Curated database of oligogenic diseases and genetic variants causing these diseases. The successor of DIDA, a similar database for digenic diseases

An open-source, curated and peer reviewed pathway database. Its goal is to provide tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling and systems biology.

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

Web interface accessing a curated database with information about biochemical reactions and kinetic properties in an experimental or environmental context.