Phospho3d

Phospho3D provides three-dimensional structural information for protein phosphorylation sites (P-sites) to support analysis and prediction of phosphorylation and its functional implications.

Key Features:

• Extensive Database: Contains a markedly expanded collection of P-site structures with an 11-fold increase from the previous version.
• Structural Comparison: Performs large-scale structural comparisons between 3D zones surrounding P-sites and a representative dataset of protein structures to identify structurally similar sites.
• Enhanced Structural Descriptors: Incorporates additional structural descriptors to enrich the annotation of each P-site.
• Non-Redundant Data Sets: Provides non-redundant sets of 3D structures to reduce redundancy and emphasize unique structural features.
• Downloadable Resources: Includes downloadable non-redundant, structurally annotated P-sites for integration into external analyses or databases.
• P3Dscan Functionality: Implements P3Dscan (version 2.0) to submit a protein structure and scan it against the curated 3D zones within Phospho3D to identify potential phosphorylation sites by structural similarity.

Scientific Applications:

• Prediction of putative phosphorylation sites: Uses structural similarity between 3D zones to suggest new candidate P-sites.
• Analysis of spatial context of phosphorylation: Facilitates investigation of the 3D environment surrounding P-sites to study structural determinants of phosphorylation.
• Study of post-translational modification effects: Supports analysis of how phosphorylation as a post-translational modification may influence protein structure and function.

Methodology:

Phospho3D is derived from the Phospho.ELM database, extracts and annotates 3D zones surrounding P-sites, computes additional structural descriptors, creates non-redundant sets of structures, performs large-scale structural comparisons against a representative dataset of protein structures, and provides P3Dscan to compare submitted protein structures to the curated 3D zones.