LIGPLOT

LIGPLOT generates schematic 2-D representations of protein-ligand complexes to depict intermolecular interactions for structural analysis.

Key Features:

• PDB input: Processes standard Protein Data Bank (PDB) file inputs to extract 3D coordinates of proteins, ligands, and nucleic acids.
• 2D diagram generation: Produces schematic 2-D diagrams from 3D coordinates representing molecular contacts and geometries.
• PostScript output: Writes output as color or black-and-white PostScript files for publication-quality figures.
• Hydrogen bonds depiction: Identifies and depicts hydrogen bonds between ligand and protein atoms.
• Hydrophobic interactions depiction: Identifies and depicts hydrophobic contacts between ligand and protein residues.
• Atom accessibilities: Reports atom accessibilities as part of the diagram annotations.
• Interaction strength visualization: Conveys relative strengths of intermolecular interactions in the schematics.
• Consistent orientation across sets: Generates multiple 2D diagrams with maintained orientation for related ligand–protein interaction sets.
• Ligand and nucleic acid support: Handles any ligand type and can represent protein–nucleic acid interactions.
• Comparative series handling: Supports analysis of series such as multiple small molecules binding the same protein or a ligand across homologous proteins, including cases where protein and ligand change.

Scientific Applications:

• Structural biology visualization: Visualizes key intermolecular interactions in protein–ligand and protein–nucleic acid complexes.
• Enzyme complex analysis: Facilitates inspection of enzyme–substrate and inhibitor binding patterns from PDB structures.
• Comparative binding studies: Enables comparison of interaction patterns across series of small molecules binding the same target.
• Homologue interaction comparison: Supports comparison of a single ligand's interactions across homologous proteins.
• Interaction annotation: Provides annotated diagrams highlighting hydrogen bonds, hydrophobic contacts, and atom accessibility for interpretation of binding determinants.

Methodology:

Reads PDB files, computes hydrogen bonds, hydrophobic interactions and atom accessibilities from 3D coordinates, generates schematic 2-D diagrams maintaining consistent orientation for related sets, and outputs color or black-and-white PostScript files.