DSSP

DSSP assigns secondary structure and residue-level structural annotations to protein entries from the Protein Data Bank (PDB) to support structural analysis and modeling.

Key Features:

• Secondary Structure Assignments: Assigns secondary structures to amino acid residues using atomic coordinates from Protein Data Bank (PDB) entries and identifies α-helices, β-strands, and turns.
• Enhanced π-Helix Recognition: Includes updates to recognize and assign π-helices within protein structures.
• Parallel Databanks: Maintains a DSSP databank that mirrors each PDB entry for consistent per-structure records.
• Additional Structural Information: Provides derived data including lists of residues involved in crystal contacts, residue accessibility, and contact definitions.
• Consistent Data Representation: Offers databanks such as BDB that contain X-ray PDB files with standardized B-factor representations.

Scientific Applications:

• Protein Structure Analysis: Enables analysis of protein folding patterns and secondary-structure distributions by residue.
• Molecular Modeling: Supplies per-residue secondary structure and accessibility data used to inform and validate computational models.
• Drug Design: Identifies accessible residues and crystal-contact information relevant to binding-site characterization and rational ligand design.
• Comparative Structural Studies: Provides consistently represented structural data across PDB entries to support comparative and evolutionary analyses.

Methodology:

Computes per-residue secondary structure assignments from atomic coordinates in PDB entries, recognizes π-helices, derives residue accessibility, crystal-contact lists and contact definitions, mirrors PDB entries in the DSSP databank, and standardizes B-factor representations in BDB X-ray PDB files.