PLIP

PLIP analyzes non-covalent interactions in protein–ligand complexes to detect and report atomic-level contacts relevant to structural bioinformatics, drug discovery, and nucleic acid interaction studies.

Key Features:

• Automated detection: A rule-based algorithm automatically identifies seven types of non-covalent interactions at the atomic level: hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges, and halogen bonds.
• Input formats: Accepts Protein Data Bank (PDB) structures, protein or ligand names, and custom protein–ligand complexes derived from docking studies, without requiring prior structure preparation.
• Output formats: Generates images, PyMOL session files, and parsable result files for downstream analysis.
• Nucleic acid interactions: Extended capability to detect interactions involving DNA and RNA in addition to protein–ligand complexes.

Scientific Applications:

• Docking evaluation: Characterizes docking experiments by identifying and reporting atomic-level contacts between proteins and ligands.
• Ligand–protein complex assessment: Assesses novel ligand–protein complexes for key non-covalent interactions relevant to lead optimization.
• DNA-targeting drug studies: Analyzes binding mechanisms of drugs interacting with DNA targets, including applications to cancer drug research.
• RNA–protein interaction analysis: Investigates interaction dynamics within RNA–protein complexes, including systems implicated in neurological diseases.

Methodology:

PLIP applies a rule-based algorithm to input PDB structures, protein or ligand names, or docking-derived complexes to identify hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges, and halogen bonds at the atomic level.