PDB-BLAST

PDB-BLAST performs sequence-based identification of protein structural homologs by searching a query protein sequence against the Protein Data Bank (PDB) using the Basic Local Alignment Search Tool (BLAST) and aligning sequence hits to their corresponding 3D structures.

Key Features:

• Two-step protocol: Implements a two-step protocol combining a sequence similarity search and subsequent structural alignment.
• Sequence similarity search (BLAST): Uses BLAST to query sequences against the Protein Data Bank (PDB) to identify sequence homologs.
• Structural alignment to PDB 3D structures: Aligns identified sequence hits with their corresponding 3D structures from the PDB to assess structural similarity.
• Integration with BLAST algorithms: Leverages BLAST’s local alignment algorithms (Basic Local Alignment Search Tool) for robust sequence comparison.

Scientific Applications:

• Protein structure prediction: Predicts probable protein structures by mapping query sequences onto known PDB structures when experimental structures are unavailable.
• Protein function annotation: Informs protein function through identification of structural homologs.
• Evolutionary analysis: Studies evolutionary relationships by identifying conserved structural features among homologous proteins.
• Structure-based drug design: Supports drug design by providing 3D conformational insights of target proteins.

Methodology:

Performs a BLAST sequence similarity search against the Protein Data Bank (PDB) followed by alignment of the identified sequence hits to their corresponding 3D structures from the PDB.