title: AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.
abstract: Knowledge about protein interaction sites provides detailed information of protein-protein interactions (PPIs). To date, nearly 20,000 of PPIs from Arabidopsis thaliana have been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain-domain interactions or domain-motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html .
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Shiping
authors.initials: S
authors.lastname: Yang
authors.affiliation: Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. soontide6825@163.com.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. zidingzhang@cau.edu.cn.
authors.forename: Ziding
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D030562:Databases, Protein; D011485:Protein Binding
chemical_list: D029681:Arabidopsis Proteins
keywords: 3D complex structure; Arabidopsis thaliana; Database; Domain–domain interaction; Domain–motif interaction; Protein interaction site