buccaneer

buccaneer traces protein chains in experimental electron-density maps to identify likely alpha-carbon (C(alpha)) positions and produce initial backbone traces for protein structure determination.

Key Features:

• Likelihood-Based Density Target Function: Employs an oriented electron-density likelihood target function applied repeatedly to locate probable C(alpha) positions within electron-density maps.
• Seed Position Identification: Locates a small set of promising seed C(alpha) positions in the map to initiate chain building.
• Chain Fragment Growth: Extends seed positions into longer chain fragments by iterative application of the likelihood target function.
• Assembly of Chain Fragments: Assembles extended chain fragments into a coherent initial chain trace.

Scientific Applications:

• Structural Biology: Automates backbone tracing from experimental electron-density maps to support protein structure determination.
• Protein Model Building: Generates initial C(alpha) traces used in model building and refinement from electron-density data.
• Drug Discovery: Provides backbone traces that facilitate structure-based drug discovery efforts.
• Enzyme Mechanism Studies: Supplies initial traces for interpretation of active-site geometry and enzyme mechanisms.
• Elucidation of Complex Biological Processes: Aids interpretation of protein structures relevant to complex biological processes by supplying initial chain traces from electron-density maps.

Methodology:

Apply an oriented electron-density likelihood target function repeatedly to locate likely C(alpha) positions; identify a small set of seed positions; iteratively grow chain fragments from seeds using the likelihood target; assemble extended fragments into an initial chain trace.