CLICK

CLICK performs topology-independent comparisons and superimpositions of biomolecular 3D structures, including proteins, DNA, RNA, and other macromolecules, to identify local structural similarities.

Key Features:

• Topology-independent comparison: Enables structural alignments that do not depend on overall topology to detect local similarities.
• Cartesian-coordinate representation: Uses Cartesian coordinates for precise structural comparisons and alignment.
• Clique identification: Detects cliques of 3 to 7 structurally similar residues as local anchors for alignment.
• Residue equivalence mapping: Establishes one-to-one residue equivalences between structures based on matched cliques.
• Additional structural features: Optionally incorporates secondary structure, solvent accessible surface area, and residue depth to refine alignments.
• Least square fitting: Applies least square fitting to superimpose aligned residues and optimize structural overlap.
• Complementary alignments: Generates complementary alignments to account for conformational variations between compared structures.
• Domain and subdomain detection: Detects similarities across structural subdomains, domains, and topological variants.
• Benchmarking performance: Has been benchmarked against other protein and RNA alignment methods with statistically significant improvements in structure overlap accuracy.

Scientific Applications:

• Protein structural comparison: Identify relationships among proteins and detect conserved or variant structural regions.
• RNA structural alignment: Align RNA 3D structures for comparative and evolutionary analyses.
• Domain and subdomain analysis: Detect conserved subdomains, domains, and structural motifs across macromolecules.
• Conformational change characterization: Recognize and account for conformational changes within domains or subdomains between structures.
• Superposition for structure-function studies: Produce precise superpositions to support downstream analyses of structure–function relationships.

Methodology:

Identifies cliques of 3–7 structurally similar residues between pairs of Cartesian-coordinate structures, uses these cliques to establish one-to-one residue equivalences, optionally integrates secondary structure, solvent accessible surface area, and residue depth to refine matches, generates complementary alignments to capture conformational variations, and applies least square fitting to superimpose the aligned residues.