FATCAT

FATCAT aligns flexible protein structures to detect hinges and conformational changes for comparative structural analysis and database searching.

Key Features:

• Flexible Structure Alignment: Identifies hinges and internal rearrangements to accommodate protein flexibility during alignment.
• Pairwise Comparison (FATCAT-pairwise): Compares two PDB-format protein structures and reports structural alignments with statistical significance as P-values.
• Database Searching (FATCAT-search): Searches structural databases to return lists of structurally similar proteins ranked by P-values and reports conformational differences.
• Optimization and Minimization: Optimizes alignments while minimizing the number of rigid-body movements (twists) around pivot points (hinges).
• Visualization and Performance (FATCAT 2.0): Offers enhanced visualization options for structural differences and faster database searches.

Scientific Applications:

• Comparative Structural Analysis: Comparing two protein structures to assess similarity for studies of protein function and evolution.
• Conformational Studies: Identifying conformational changes and internal rearrangements to investigate functional mechanisms and interactions.
• Database Searches for Similar Structures: Discovering structurally similar proteins to explore protein families and evolutionary relationships.

Methodology:

Alignments are performed using Flexible structure AlignmenT by Chaining AFPs with Twists (FATCAT) that identify hinges and internal rearrangements; the algorithm optimizes alignments while minimizing the number of rigid-body twists around pivot points; pairwise comparisons operate on PDB-format structures and report P-values, and database searches return structures ranked by P-values.