Refine
Has Fulltext
- yes (13)
Is part of the Bibliography
- yes (13)
Document Type
- Journal article (13)
Keywords
- DNA storage (2)
- SARS-CoV-2 (2)
- 6-benzylaminopurine (1)
- Aspergillus (1)
- Aspergillus fumigalus (1)
- B-cell (1)
- CETCH cycle (1)
- CO2-sequestration (1)
- COVID-19 (1)
- DNA (1)
- Gene expression vectors (1)
- Klimaneutralität (1)
- Klimapflanzen (1)
- Klimawandel (1)
- MHC I (1)
- MHC II (1)
- Polymerase chain reaction (1)
- R0 (1)
- RNA (1)
- Sanger sequencing (1)
- Shotgun method (1)
- Synthetic biology (1)
- T-cell (1)
- T-cell epitope (1)
- Virtual sequencing (1)
- biofuel (1)
- biomanufacturing (1)
- carboxylation (1)
- computational (1)
- computational modelling (1)
- cytokinins (1)
- data storage (1)
- dendritic cells (1)
- design (1)
- drug design (1)
- dynamic protein-protein interactions (1)
- elementary modes (1)
- engineering (1)
- enzyme (1)
- epitope mapping (1)
- epitope prediction (1)
- evolution (1)
- immune-informatics (1)
- infection (1)
- infection spread (1)
- lethality rate (1)
- light-gated proteins (1)
- metabolic modeling (1)
- metabolic modelling (1)
- metabolic pathways (1)
- metabolism (1)
- microbes (1)
- mortality (1)
- nanocellulose (1)
- natural processing (1)
- network simulation (1)
- oncolytic virus (1)
- optogenetics (1)
- photorespiration (1)
- population coverage (1)
- positive selection (1)
- protein analysis (1)
- protein chip (1)
- signalling (1)
- signalling pathways (1)
- single-electron transistors (1)
- synthetic biology (1)
- synthetic pathways (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (13)
- Institut für Informatik (2)
- Institut für Virologie und Immunbiologie (2)
- Center for Computational and Theoretical Biology (1)
- Institut für Experimentelle Biomedizin (1)
- Institut für Pharmakologie und Toxikologie (1)
- Kinderklinik und Poliklinik (1)
- Klinik und Poliklinik für Anästhesiologie (ab 2004) (1)
EU-Project number / Contract (GA) number
- 031A408B (1)
- ESF-ZDEX 4.0 (1)
PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.