ArchSchema

ArchSchema visualizes protein domain architectures using Pfam annotations and generates dynamic 2D network plots that link domain architectures to Protein Data Bank (PDB) structural information and associated UniProt or PDB codes.

Key Features:

• Pfam annotation visualization: Visualizes protein domain architectures using Pfam annotations.
• Dynamic 2D network plots: Generates dynamic 2D network plots where nodes correspond to distinct Pfam domain architectures.
• Node representation: Depicts each architecture node as a sequence of colored boxes representing constituent Pfam domains.
• PDB mapping: Annotates nodes with whether corresponding 3D structural information exists in the Protein Data Bank (PDB).
• Satellite nodes: Includes satellite nodes that display UniProt codes or PDB codes for proteins sharing a specific architecture.
• Search by identifier: Supports queries by UniProt code or Pfam domain identifier to locate protein sequences of interest.
• Filtering options: Offers filtering by domain specificity, organism, or presence in the PDB.
• Sequence-structure integration: Integrates sequence-based Pfam annotations with PDB structural mappings for comparative analysis.

Scientific Applications:

• Domain-architecture analysis: Supports analysis of protein domain architectures in bioinformatics and structural biology studies.
• Structural annotation mapping: Enables mapping of domain architectures to available 3D structures in the PDB.
• Evolutionary relationship exploration: Facilitates exploration of evolutionary relationships among proteins based on shared architectures.
• Functional prediction: Aids functional prediction by linking domain composition to known structures.
• Interaction inference: Supports inference of potential interactions within protein families via architecture similarity.
• Targeted retrieval and analysis: Enables targeted retrieval and analysis of proteins using UniProt or Pfam queries and filters.

Methodology:

Constructs dynamic 2D network plots from Pfam annotations where nodes represent distinct Pfam domain architectures depicted as sequences of colored boxes, annotates nodes with PDB presence and attaches satellite nodes with UniProt or PDB codes, and supports queries by UniProt code or Pfam domain identifier plus filtering by domain specificity, organism, or PDB presence.