PlaPPISite

PlaPPISite provides detailed annotations of protein-protein interaction (PPI) sites across 13 plant species—Chlamydomonas reinhardtii, Arabidopsis thaliana, Ricinus communis, Glycine max, Oryza sativa, Solanum lycopersicum, Solanum tuberosum, Vitis vinifera, Zea mays, Brachypodium distachyon, Selaginella moellendorffii, Populus trichocarpa, and Medicago truncatula—by integrating experimentally verified and predicted PPIs for structural and functional analysis.

Key Features:

• Comprehensive interaction dataset: Compiles 121 experimentally verified protein complex structures and constructed complex structures derived from experimental or predicted PPIs across the 13 plant species.
• Interaction site annotation: Annotates PPI sites with 3D structural contexts where available and infers domain-domain interactions (DDIs) and domain-motif interactions (DMIs) when 3D models are absent.
• Reliability assessment: Provides source species of interolog templates, Gene Ontology (GO) annotations, subcellular localization, and gene expression similarity for evaluating predicted PPIs.
• Visualization of molecular interactions: Supplies visualization of protein complexes, interaction sites, and protein interaction networks for structural and network inspection.
• Homology modelling and annotation: Supports homology modelling and annotation of protein interaction sites within protein complexes to extend structural coverage.

Scientific Applications:

• Cross-species PPI analysis: Enables comparison of conserved and species-specific PPIs across the 13 plant species.
• Structural interface studies: Facilitates analysis of interface residues and 3D contexts using experimentally verified and modelled complex structures.
• Functional inference of interactions: Integrates GO annotations, subcellular localization, and expression similarity to infer functional roles of PPIs.
• Assessment of predicted PPIs: Supports evaluation of predicted interactions using interolog template provenance and multiple supporting annotations.

Methodology:

Compilation of 121 experimentally verified complex structures and constructed complexes from experimental or predicted PPIs; annotation of interaction sites with 3D structural context; inference of DDIs and DMIs for interactions lacking 3D models; use of interolog templates, GO annotations, subcellular localization, and gene expression similarity for reliability assessment; homology modelling for interaction-site annotation.