PDBFINDER reformatted PDB files

PDBFINDER reformatted PDB files provides computationally derived, reformatted entries based on Protein Data Bank (PDB) records that expose administrative records and multiple parallel databanks (HSSP, PDBREPORT, PDB_REDO, DSSP, BDB) to support structural analyses of residues, crystal contacts, residue accessibility, π-helices, and consistent B-factors.

Key Features:

• Parallel Databanks: Each entry corresponds directly to a PDB entry, enabling parallel mapping between PDB records and derived databanks focused on administrative information rather than atomic coordinates.
• Enhanced Databanks: Established databanks such as HSSP, PDBREPORT, and PDB_REDO have been updated and the DSSP databank software has been rewritten to better handle π-helices.
• Newly Added Databanks: Includes databanks listing residues involved in crystal contacts, contacting residues defined by multiple contact criteria, and residue accessibility data.
• Consistent Data Representation: The BDB databank presents X-ray PDB files with consistently represented B-factors to facilitate comparative analyses.
• Administrative Record Formatting: Entries provide structured, search-engine-friendly formatted administrative records extracted or reformatted from PDB files.

Scientific Applications:

• Structural Analysis: Enables analysis of protein secondary structure elements, including π-helices, and other structural features derived from PDB entries.
• Protein–Protein Interactions: Provides residue contact lists and crystal-contact annotations to support studies of molecular interfaces.
• Drug Design and Development: Supplies refined structural and accessibility data to aid identification of potential targets and structure-based design considerations.

Methodology:

Computationally derived databanks are generated from PDB entries; existing software was rewritten for improved accuracy in the DSSP databank to better annotate π-helices; new algorithms were developed to produce residue accessibility and contact-definition datasets.