Services: Proteins And Proteomes

A collection of high-resolution three-dimensional structural templates for domain-domain interactions. It contains templates for interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab.

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

APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). 

Web portal for the annotation of pathological protein variants.

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

Predicts the subcellular localization of proteins in eukaryotes.

Either as a cooperation or consultancy service.

Website offering a comprehensive framework for constructing Biophysical Proteomes.

Primer design and ePCR method for bisulfite treated and untreated DNA sequences (cDNA, genomic)

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. 

Tools for processing the topology and structure of transmembrane proteins

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

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.

DoGSite is a grid-based method which uses a Difference of Gaussian filter to detect potential protein binding pockets - solely based on the 3D structure of the macromolecules.

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. 

FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.

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.

FLASHIda is an intelligent online data acquisition algorithm for top-down proteomics (TDP) that ensures the real-time selection of high-quality precursors of diverse proteoforms. 

FLASHQuant performs MS1-level label-free quantification data analysis in top-down proteomics, with an automatic overlapping signal resolution method.