BSDD

BSDD searches and visualizes user-defined sequence motifs within Protein Data Bank (PDB) structures to support structural analysis using non-homologous datasets at 25% and 90% sequence identity.

Key Features:

• User-Defined Motif Search: Searches user-provided sequence motifs or fragments against the PDB collection of protein structures.
• Non-homologous PDB Datasets: Provides access to non-homologous protein structure sets at 25% and 90% sequence identity.
• Visualization with RASMOL: Renders three-dimensional views of identified motifs using the RASMOL graphics package to examine spatial arrangements and conformations.
• Atomic Coordinate Extraction: Extracts atomic coordinates for user-defined motifs and enables saving of coordinate files to the client system.
• Regular Data Updates: Updates atomic coordinates weekly from the RCSB-PDB server.

Scientific Applications:

• Comparative Structural Analysis: Enables examination of motifs across non-homologous proteins to identify structural conservation or variation.
• Drug Design and Discovery: Facilitates identification of potential binding sites and structural features relevant to therapeutic targeting.
• Protein Engineering: Supports visualization and extraction of structural information needed for precise protein modification and design.

Methodology:

Performs sequence motif searches against PDB structures, extracts corresponding atomic coordinates, renders structures with RASMOL, and refreshes coordinate data weekly from the RCSB-PDB server.