Research Area: Modeling & Prediction


Our work currently concentrates on modeling and predicting protein region interactions that underlie protein interactions. In particular, protein domains are of great importance for the function and structure of interactions as well as for ligand and drug binding. We are also interested in understanding protein complexes as essential cellular machines for systems biology research and in simulating their functional role in molecular processes as well as their dynamic formation and composition. Additionally, we devise novel visual analytics methods for elucidating protein structure-function relationships using residue interaction networks and our new Cytoscape plugin RINalyzer.

We developed the Cytoscape plugin DomainGraph that decomposes interacting proteins into their respective regions (domains) and computes a putative network of corresponding domain-domain interactions. In addition, DomainGraph supports the integration of exon expression data measured using Affymetrix GeneChip microarrays or next-generation RNA sequencing. This feature allows the analysis of alternative splicing events and the characterization of their dynamic effects on protein and domain interaction networks. To this end, the research group cooperates with biological and medical groups from Europe and USA.

Recently, we have introduced new methods to determine high-confidence physical protein contacts within protein complexes and to model both domain-domain and domain-peptide interactions of proteins. We have also presented a novel functional similarity measure based on the Gene Ontology (GO) to derive useful confidence score thresholds for predicted domain-domain interactions. This measure is integrated into our GOTax platform and the well-known Pfam search engine.

Contact: Dr. Mario Albrecht (E-mail:

Bioinformatics Cooperation Partners


  1. Doncheva, N.T., Assenov, Y., Domingues, F.S., Albrecht, M.
    Topological analysis and interactive visualization of biological networks and protein structures.
    Nature Protocols, 7(4):670-685, 2012.
    (Abstract) (Press article in English) (Press article in German)

  2. Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M.
    Analyzing and visualizing residue networks of protein structures.
    Trends in Biochemical Sciences, 36(4):179-182, 2011.
    (Abstract) (Press release) (Press article in English) (Press article in German)

  3. Schelhorn, S.E., Mestre, J., Albrecht, M., Zotenko, E.
    Inferring physical protein contacts from large-scale purification data of protein complexes.
    Molecular & Cellular Proteomics, 10(6):M110.004929.1-15, 2011.
    (Abstract) (Supplement)

  4. Emig, D., Sander, O., Mayr, G., Albrecht, M.
    Structure collisions between interacting proteins.
    PLoS ONE, 6(6):e19581.1-7, 2011.
    (Abstract) (Supplement)

  5. Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B.R., Albrecht, M.
    AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
    Nucleic Acids Research, 38(Web Server issue):W755-W762, 2010.
    (Abstract) (Press release) (Newsletter)

  6. Schelhorn, S.E., Lengauer, T., Albrecht, M.
    An integrative approach for predicting interactions of protein regions.
    Bioinformatics, 24(16):i35-i41, 2008.
    (Abstract) (Supplement) (First presented and published at the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 2008.)

  7. Emig, D., Cline, M.S., Lengauer, T., Albrecht, M.
    Integrating expression data with domain interaction networks.
    Bioinformatics, 24(21):2546-2548, 2008.

  8. Emig, D., Cline, M.S., Klein, K., Kunert, A., Mutzel, P., Lengauer, T., Albrecht, M.
    Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.
    Journal of Integrative Bioinformatics, 5(2):101.1-15, 2008.
    (Abstract) (First presented and published at the 5th Annual Meeting of the International Symposium on Integrative Bioinformatics (IB08), Lutherstadt Wittenberg, Germany, 2008.)

  9. Emig, D., Klein, K., Kunert, A., Mutzel, P., Albrecht, M.
    Visualizing domain interaction networks and the impact of alternative splicing events.
    In Proceedings of the 5th International Conference on BioMedical Visualization (MediVis): Information Visualization in Medical and Biomedical Informatics, IEEE Computer Society, Los Alamitos, CA, USA, ISBN 978-0-7695-3284-4, 36-43, 2008.
    (Abstract) (First presented and published at the Symposium on Information Visualization in Biomedical Informatics (IVBi) as part of MediVis, London, United Kingdom, 2008.)

  10. Schlicker, A., Huthmacher, C., Ramírez, F., Lengauer. T., Albrecht, M.
    Functional evaluation of domain-domain interactions and human protein interaction networks.
    Bioinformatics, 23(7):859-865, 2007.
    (Abstract) (Supplement) (First published in Proceedings of the German Conference on Bioinformatics (GCB), Tübingen, Germany, 2006:
    GI-Edition - Lecture Notes in Informatics (LNI), Köllen Verlag, Bonn, Germany, ISBN 978-3-88579-177-5, P-83:115-126, 2006.)

  11. Schlicker, A., Rahnenführer, J., Albrecht, M., Lengauer, T., Domingues, F.S.
    GOTax: investigating biological processes and biochemical activities along the taxonomic tree.
    Genome Biology, 8(3):R33.1-10, 2007.
    (Abstract) (Supplement)

  12. Albrecht, M., Huthmacher, C., Tosatto, S.C.E., Lengauer, T.
    Decomposing protein networks into domain-domain interactions.
    Bioinformatics, 21(Suppl. 2):ii220-ii221, 2005.
    (Abstract) (Supplement) (First published at the 4th European Conference on Computational Biology (ECCB), Madrid, Spain, 2005.)