Fragger

Fragger enables efficient querying and management of 3D protein fragment databases for protein modeling and design.

Key Features:

• Database Creation and Querying: Create custom fragment databases from any set of PDB files, including specified subsets and unpublished structures, supporting all fragment lengths.
• Efficient Fragment Search: Rapidly search a fragment database with a query fragment and a user-specified distance threshold, returning matches ranked by proximity to the query.
• Handling Structural Gaps: Accommodate query fragments that contain structural gaps during matching.
• Sequence Constraints: Filter matches using regular expressions composed of one-letter amino acid codes.
• High-Throughput RMSD Computation: Compute backbone Root Mean Square Deviation (RMSD) between a single query fragment and multiple database fragments in high-throughput mode.

Scientific Applications:

• Protein design: Retrieve structurally compatible fragments to inform design of protein backbones and local motifs.
• Loop grafting: Identify candidate loop fragments for grafting onto target structures.
• Structural motif identification: Search PDB-derived fragment libraries to detect recurring 3D motifs.
• Comparative structural analysis: Use backbone RMSD and distance-threshold ranking to compare fragment conformations and study protein function and interaction dynamics.
• Targeted searches within PDB subsets: Query specific subsets of the Protein Data Bank (PDB), including unpublished structures.

Methodology:

Build customizable databases from selected PDB files and match query fragments to database entries by structural similarity using a distance threshold, with support for gaps and sequence-constraint filtering (regular expressions of one-letter amino acid codes), and perform high-throughput backbone RMSD computations.