PatchFinder

PatchFinder identifies highly conserved protein surface regions to predict functional sites involved in substrate, ligand, and protein interactions.

Key Features:

• Detection of Functional Regions: PatchFinder employs an algorithm to detect conserved surface patches on protein structures that are likely involved in interactions with substrates, ligands, or other proteins.
• Superior Performance: Comparative analysis on a dataset of annotated proteins shows PatchFinder outperforms similar methods in accurately identifying functional surface regions.
• N-Func Database Integration: PatchFinder collects structures of hypothetical proteins together with their predicted functional regions and compiles this information in the N-Func database.

Scientific Applications:

• Functional Site Annotation: Predicts and annotates functional regions on proteins of unknown function, including hypothetical proteins.
• Interface and Nucleotide-Binding Inference: Suggests potential interprotein interfaces and nucleotide-binding sites based on conserved surface patches.
• Drug Discovery: Supports target identification and binding-site characterization relevant to drug discovery.
• Enzyme Engineering: Identifies active or substrate-binding regions to guide enzyme engineering.
• Protein–Protein Interaction Studies: Aids study of protein-protein interactions by highlighting conserved interaction surfaces.

Methodology:

Uses an improved version of the original PatchFinder algorithm to systematically analyze protein structures for conserved surface regions, with predictions validated against a dataset of annotated proteins.