Services: Molecular And Cellular Structures

Predicts protein stability changes upon single point mutation from protein structure or protein sequence.

Web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server offers a variety of methods to explore nucleic acid flexibility, from coarse-grained low resolution mesoscopic models to atomistic molecular dynamics simulations.

IntOGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.

InterPro classifies proteins into families and predicts the presence of important domains and sites.

iPath is a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, iPATH thus allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets. Part of the Microbiome Analysis Toolbox. 

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

A java tool for profiling short-read sequences from T cell receptors and immunoglobulins

A method for estimating disordered stretches in transmembrane proteins

Open-source infrastructure service for research and engineering of metabolism in model organisms and human

METALizer predicts the coordination geometry of metals in metalloproteins.

The MHC Motif Atlas helps visualize, analyse, and compare the different binding specificities of thousands of class I and class II MHC molecules, and includes binding motifs, peptide length distributions, motifs of phosphorylated ligands, multiple specificities, or links to X-ray crystallography structures.

The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates. Missense3D predicts the structural changes introduced by an amino acid substitution.

A database of protein disorder and mobility annotations, designed centralize resources for annotations of intrinsic protein disorder and its function. Part of the InterPro consortium, an ELIXIR Core Data Resource.

Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies. 

Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis. 

A web application for validation of annotation of ligands and
residues.

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

Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences;

Software to identify defined fragments in biomacromolecules.

Database of membrane localization of transmembrane proteins with defined spatial structure

Predictor of human deleterious Single Nucleotide Polymorphisms.

A suite of tools available on the web to predict and analyze protein structure, function and mutations. 

An open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables.

The Protein Model Database stores manually built 3D models of proteins.

The Protein Data Bank in Europe (PDBe) is the European part of the wwPDB for the collection, organisation and dissemination of data on biological macromolecular structures.

A PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools.

A database of annotated tandem repeat protein structures, combining computer-based methods and manual curation.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.

Residue interaction network generator. RING identifies all types of non-covalent interactions at atomic level in a protein structure (PDB);

Web tool for prediction of rRNA secondary structures.