Drug ReposER

Drug ReposER identifies potential alternative protein targets for existing drugs by comparing 3D binding-site substructure similarities in Protein Data Bank (PDB) protein structures.

Key Features:

• 3D Substructure Similarity Analysis: Utilizes pre-computed amino acid arrangements from Protein Data Bank (PDB) structures to compare 3D binding-site substructures to known drug binding sites.
• Potential Target Identification: Pinpoints alternative protein targets for existing drugs by matching binding site structures.
• Sidechain Superposition Mapping: Maps matched sidechain superpositions to identify similar binding-site configurations across proteins.
• Visualization: Integrates the NGL viewer to visualize molecular search results and structural similarities.

Scientific Applications:

• Drug repositioning: Identifies proteins with binding sites similar to known drug targets to suggest novel therapeutic uses for existing compounds.
• Target discovery for experimental follow-up: Generates candidate alternative protein targets based on structural similarity for downstream experimental validation.

Methodology:

Uses pre-computed amino acid arrangements from PDB, performs 3D substructure similarity comparisons between protein binding sites and known drug-binding sites, and maps matched sidechain superpositions, with results visualized via the NGL viewer.