PIC

PIC computes inter-residue interactions from three-dimensional protein coordinate sets to identify and quantify disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulfur interactions, cation-π interactions, residue accessible surface area, and residue depth in protein structures and complexes.

Key Features:

• Interaction Calculation: Computes disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulfur interactions, and cation-π interactions.
• Interaction Criteria: Applies predefined, literature-derived criteria for detection and quantification of interactions.
• Accessible Surface Area and Depth: Calculates residue accessible surface area and residue depth relative to the protein surface.
• Visualization Output: Produces output compatible with RasMol and Jmol for visualization of identified interactions.
• Custom Interaction Recognition: Supports specification and detection of particular interaction types such as apolar-apolar and ionic interactions and their classification by structural context (buried versus exposed residues).

Scientific Applications:

• Protein Stability: Provides interaction data to assess contributions of specific bonds and contacts to protein stability.
• Protein Folding: Enables analysis of intramolecular interactions relevant to folding pathways and intermediate states.
• Protein Function and Complex Formation: Characterizes residue interactions that mediate function and assembly of protein complexes.
• Structural Interpretation: Maps residue-level interactions and accessibility to interpret structural integrity and functional dynamics.

Methodology:

Accepts three-dimensional coordinate sets of a protein or assembly as input and processes them using predefined, literature-derived criteria to compute inter-residue interactions and accessibility metrics.