pKNOT-v2

pKNOT-v2 detects and characterizes knotted regions in protein structures and predicts 3D structures from amino acid sequences using homology modeling to enable analysis of protein topology.

Key Features:

• Knot Detection: Employs Taylor's smoothing algorithm to identify knotted regions within protein chains.
• Homology Modeling Tool: Generates 3D structural models from protein sequences via homology modeling.
• Updated Database: Maintains a database of knotted proteins compiled from current PDB entries using automated and manual procedures.
• Visualization: Provides Java-based 3D graphics visualization of detected knots.

Scientific Applications:

• Topology analysis: Characterizes protein topology and annotates knotted motifs for studies of structure–function relationships.
• Case studies: Enables analysis of knots in proteins such as the chromophore-binding domain of phytochrome, ketol-acid reductoisomerase, and SpoU methyltransferase.
• Structure prediction: Allows investigation of hypothetical or uncharacterized proteins by predicting 3D models from sequences.
• Research support: Supports structural biology, protein engineering, and evolutionary studies through knot annotation and modeled structures.

Methodology:

Uses Taylor's smoothing algorithm for knot detection; integrates homology modeling for predicting 3D structures from sequences; compiles the database from PDB entries via automated and manual curation; uses a Java-based 3D graphics viewer for visualization.