HSSP

HSSP provides homology-derived multiple sequence alignments and secondary-structure information for Protein Data Bank (PDB) protein entries to support comparative structural analysis and inference of conserved structural features.

Key Features:

• Multiple Sequence Alignment: HSSP generates detailed alignments of sequences homologous to PDB entries to facilitate comparative analyses.
• Homology-Based Secondary Structure Information: HSSP derives secondary-structure annotations from homologous sequences to extend structural information beyond experimental data.
• Integration with Other Databases: HSSP is part of a suite running parallel to the PDB and integrates with DSSP, PDBREPORT, PDBFINDER, PDB_REDO, and WHY_NOT.
• Regular Updates: The database is updated weekly to reflect current PDB entries and their homologous alignments.

Scientific Applications:

• Structural Genomics: Use alignments to explore evolutionary relationships and generate functional predictions for protein families.
• Cancer Biology: Analyze structures and homologs to identify potential therapeutic targets and understand molecular effects of cancer-related mutations.
• Protein Design: Provide structural conservation and alignment context to inform design of novel proteins with desired functions.

Methodology:

HSSP derives secondary-structure information by generating homology-based multiple sequence alignments of PDB sequences with their homologs.