title: SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.
abstract: BACKGROUND
  Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date.
  
  
  METHODS
  We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category.
  
  
  CONCLUSIONS
  SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.
authors.affiliation: Korean BioInformation Center, KRIBB, Daejeon 305-806, Korea. kimplove@kribb.re.kr
authors.forename: Woo-Yeon
authors.initials: WY
authors.lastname: Kim
authors.forename: Sungsoo
authors.initials: S
authors.lastname: Kang
authors.forename: Byoung-Chul
authors.initials: BC
authors.lastname: Kim
authors.forename: Jeehyun
authors.initials: J
authors.lastname: Oh
authors.forename: Seongwoong
authors.initials: S
authors.lastname: Cho
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
authors.forename: Jong-Soon
authors.initials: JS
authors.lastname: Choi
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D003628:Database Management Systems; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods*; D046939:Synechocystis / Q000378:metabolism*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins