Chair of Bioinformatics


PRO-Simat is a powerful all-in-one web tool designed for analyzing protein interaction networks, exploring their dynamic changes, and facilitating pathway engineering. With access to an extensive integrated database comprising over 8 million protein-protein interactions across 32 model organisms and the human proteome, PRO-Simat offers a range of functionalities to enhance protein network analysis. These include

Pathway analysis: The tool incorporates GO enrichment and KEGG pathway analyses, enabling users to gain valuable insights into the biological significance of protein interactions. Network structure: Interactome and visualization features allow for a clear and intuitive representation of the analyzed networks. Pathway and protein design experiments from the oncolytic virus to a DNA storage chip or novel carbon-harvesting climate plants can easily be planned and studied.

Dynamics: A key feature of PRO-Simat is its integration of dynamical network simulation through the Jimena framework. This efficient simulation method accurately models Boolean genetic regulatory networks, providing simulation outputs that include a comprehensive analysis of the type, strength, duration, and pathway of protein interactions. Users can easily modify and analyze the effects of network modifications and engineering experiments within the tool.

For more information please read the full paper:
Salihoglu R, Srivastava M, Liang C, Schilling K, Szalay A, Bencurova E, Dandekar T. PRO-Simat: Protein network simulation and design tool. Comput Struct Biotechnol J. 2023 Apr 26;21:2767-2779. doi: 10.1016/j.csbj.2023.04.023. PMID: 37181657; PMCID: PMC10172639.

direct link to the software: