FLAPP

FLAPP performs rapid, atomic-precision alignments of protein binding sites to enable large-scale structural comparison and functional inference.

Key Features:

• Rapid Alignment: Aligns a typical pair of binding sites in approximately 12.5 milliseconds on a single CPU core and about 1 millisecond using 12 cores.
• Scalability: Capable of scanning the Protein Data Bank (PDB) at scale, completing PDB-wide scans in approximately 1–2 minutes.
• Algorithmic Innovation: Implements clique matching in graphs combined with optimizations for modern CPU architectures to achieve high-speed performance.

Scientific Applications:

• Protein Function Analysis: Enables inference of protein function through atomic-level comparison of binding site arrangements.
• Drug Discovery and Development: Supports drug target identification and off-target analysis, informing polypharmacology studies.
• Structural Bioinformatics Research: Facilitates exhaustive PDB-wide structural comparisons across millions of site pairs.

Methodology:

Uses clique matching in graphs and optimizations for modern CPU architectures with multi-core parallelism; validated at multiple levels of complexity and demonstrated in a case study on vitamin B12 binding sites.