SAS

SAS annotates protein sequences with structural information derived from Protein Data Bank (PDB) entries to identify distant homologues and infer structural features such as secondary structure, interatomic contacts, and active sites.

Key Features:

• Structural annotation transfer: Applies structural information from known Protein Data Bank (PDB) structures to annotate uncharacterized protein sequences.
• Homologue search and alignment: Searches and aligns query sequences to homologous proteins with known structures to identify distant homologues.
• Annotated outputs: Generates annotated sequence files that incorporate residue-level structural features.
• Residue-level structural labels: Annotates residues by structural properties including secondary structure elements (alpha-helices, beta-sheets), interatomic contacts, and active site information, encoding these annotations as color-coded residue labels.
• Structure inspection: Performs inspection and annotation of individual structures to analyze specific structural properties.
• 3D conformation and function inference: Provides context for potential three-dimensional conformation and functional properties by mapping PDB-derived structural features onto sequences.

Scientific Applications:

• Comparative structural genomics: Enables comparison of sequence-derived annotations across proteins to study structural conservation and variation.
• Structural biology studies: Supports detailed analysis of structural features and residue-level properties within individual proteins.
• Drug discovery: Highlights active sites and contact regions that can inform target identification and ligand-binding analyses.
• Functional annotation of novel proteins: Assists in assigning structural context and potential functional sites to uncharacterized sequences.
• Evolutionary studies: Facilitates identification of distant homologues and evolutionary relationships based on transferred structural information.

Methodology:

Performs searches and sequence alignments against proteins with known structures from the Protein Data Bank (PDB), maps structural features (secondary structure, interatomic contacts, active sites) onto query sequences, and outputs annotated sequence files with residue-level annotations (including color-coding).