Software

We have developed a number of large and well-used software tools. Currently, our efforts go mainly into PLIP, the Protein-Ligand Interaction Profiler. PLIP is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures. PLIP is online and its code is open source. https://plip.biotec.tu-dresden.de/

In the past we have developed tools in textmining, structure, and networks. GoPubMed was a  novel semantic search engine, which helps answering questions using ontologies. It linked a biomedical taxonomy with articles in PubMed. It led to the spin-off Transinght GmbH, which was operational for over a decade. GoPubMed was used by many thousand users per months and its technology was employed by companies such as Bayer, Roche, Unilever, and BASF. Part of the engine was also an ontology editor, which automatically predicted well suited terms and definitions, which was incorporated into OBO-edit, a main editor for biomedical ontologies.

Regarding protein structure, we developed the first structural protein interaction database, SCOPPI, which mapped all interacting domains. Related tools were

• metaPocket, a meta server to identify ligand binding sites on protein surface,
• META-PPI, a meta-server to predict protein interction interfaces,
• Ligsitecsc, which predicts ligand binding sites based on pocket size and conservation, and
• Memotif, a database of linear motifs in alpha-helical membrane proteins.

We also developed a tool for the analysis of protein interaction networks called PowerGraphs. It finds modules in networks and employs a novel visualisation for them.

All of the above algorithms and tools are documented in our papers. However, we no longer maintain and support them