ProBiS-ligands

ProBiS-ligands predicts ligand binding to protein structures by exploiting structural similarity between binding sites to transpose ligands from template structures in the Protein Data Bank (PDB) into query binding sites.

Key Features:

• Binding-site similarity analysis: Identifies proteins with binding sites similar to a query protein structure or a selected query site by searching the Protein Data Bank (PDB) for templates with comparable binding-site geometry and local structural features.
• Template-based ligand prediction: Superimposes the query protein onto each template and transposes ligands present in template binding sites into the query binding site to yield candidate ligands compatible with the target site.
• Support for drug repurposing: Transfers known compounds from structurally similar binding sites to highlight candidates for drug repurposing based on binding-site compatibility.

Scientific Applications:

• Drug discovery and development: Prioritization of candidate ligands and binding hypotheses to inform early-stage discovery and screening workflows.
• Structural biology research: Analysis of protein–ligand interaction patterns and generation of mechanistic hypotheses informed by binding-site similarity.
• Broad applicability across proteins: Use of PDB templates enables application across diverse protein families and targets represented in structural databases.

Methodology:

Search the PDB for template proteins with similar binding-site geometry and local structural features; superimpose the query protein onto each template; transpose template ligands into the query binding site to produce candidate ligands.