WHAT IF

WHAT IF provides a suite of databases that complement the Protein Data Bank (PDB) by annotating secondary structure, generating multiple sequence alignments, assessing structural quality, re-refining X-ray structures, summarizing PDB content, and explaining failed file productions for structural and comparative analyses.

Key Features:

• Operation with PDB: Operates in parallel with the Protein Data Bank (PDB) to enhance and complement macromolecular structure data.
• DSSP: Stores secondary-structure annotations of proteins, including alpha-helices, beta-sheets, and turns.
• PDBREPORT: Produces comprehensive reports that identify errors and assess the reliability of PDB protein structures.
• HSSP: Provides multiple sequence alignments for all proteins available in the PDB to support evolutionary and comparative analyses.
• PDBFINDER: Supplies easy-to-parse summaries of PDB file content augmented with essential information from other suite databases.
• PDB_REDO: Contains re-refined versions of protein structures originally solved by X-ray crystallography to improve accuracy and resolution.
• WHY_NOT: Documents explanations for why certain files could not be produced or refined.
• Update frequency: Databases are updated weekly to maintain current structural information.

Scientific Applications:

• Structural genomics: Enables annotation, comparison, and quality assessment of macromolecular structures for structural genomics projects.
• Cancer biology: Provides structural annotations and quality-controlled models relevant to studies in cancer biology.
• Protein design: Supplies refined structures and structural annotations that support protein design and engineering.
• Evolutionary and comparative analyses: Supports study of evolutionary relationships, functional similarities, and phylogenetic analyses via HSSP alignments and DSSP annotations.
• Structure validation and selection: Facilitates selection of reliable structural models through PDBREPORT quality assessments and PDB_REDO re-refinements.

Methodology:

Secondary-structure assignment (DSSP), structure quality reporting and error identification (PDBREPORT), multiple sequence alignment generation (HSSP), concise PDB content summarization augmented with other suite data (PDBFINDER), re-refinement of X-ray crystallography structures (PDB_REDO), and explanations for failed file production or refinement (WHY_NOT).