Scientific Tools

CPR has developed several tools to aid research in proteins. The tools span from molecular networks and protein annotation to text mining and disease trajectories and are freely available for the scientific community:

Network biology tools

STRING

Database for known and predicted protein-protein interactions
Diseases

Database with disease-gene associations from text mining

Database with disease-gene associations from text mining
Cytoscape StringApp

Visualize protein interaction data

Tissues

Protein expression database focusing on protein localization at the anatomical level
COMPARTMENTS

Protein localization database focusing on protein localization at the subcellular level

Videos and training material on STRING and Cytoscape from Jensen Lab

Systems medicine tools

Disease Trajectory Browser

Explore population-wide disease progression patterns

miRandola

Classification of extracellular circulating non-coding RNA types

Sequence analysis tools

SignalP 5.0

Software that predicts the presence of signal peptides
VAMB

Algorithm using variational autoencoders for metagenomics binning

Clinical Proteomics tools

Clinical knowledge graph

A knowledge graph to interpret clinical proteomics data

Other tools

TAGGER

Highly optimized dictionary-based tagging engine for PubMed abstracts
Proteomes of life

Easy access to the data of the "proteome landscape of life“ project