How to Use juProt & Its Applications

Protocol

1. Prepare PDB Files: Obtain two protein-ligand complex PDB files (e.g., experimental structures from RCSB PDB or docked complexes from molecular docking experiments). Ensure HETATM records for ligands are present.
2. Access the App: Visit juProt at https://juprot.info/.
3. Upload Files:
   • Upload the first PDB file under "First Complex PDB File".
   • Upload the second PDB file under "Second Complex PDB File".
   • Click "Load Ligands".
4. Select Ligands:
   • juProt will auto-detect potential ligands from each PDB.
   • Select the specific ligand of interest from the dropdown menu for each complex.
   • Click "Run Analysis".
5. View Results:
   • Examine the textual "Analytical Summary" for a quick overview.
   • View the "Residue Interaction Plot" for a visual comparison of interaction frequencies per residue.
   • Download the "Comparison Table (CSV)" for a structured summary of differences and commonalities.
   • Download "Detailed Interactions (CSV)" for a complete list of all interactions for both complexes with their geometric parameters.

Applications & Use Cases for juProt

juProt is designed to provide rapid comparative insights into protein-ligand interactions, with a comprehensive focus on the full interactome (Hydrogen bonds, Hydrophobic contacts, Salt Bridges, Pi-Stacking, etc.).

1. Understanding the Impact of Mutations

Scenario: You have a wild-type protein-ligand structure and a mutant form (e.g., from a SNP or site-directed mutagenesis) bound to the same ligand.

How juProt Helps: Compare the native-ligand and mutant-ligand complexes. juProt highlights how the mutation alters the interaction network, which can help explain changes in binding affinity, drug efficacy, or resistance mechanisms. (e.g., comparing a wild-type kinase-inhibitor complex with a gatekeeper mutant-inhibitor complex).

2. Comparing Different Ligands to the Same Target

Scenario: You have several drug candidates or chemical probes binding to the same protein target.

How juProt Helps: Compare Protein+LigandA with Protein+LigandB. juProt helps identify which ligand forms more/different interactions and which residues are key common or unique interaction partners, aiding in SAR studies and lead optimization.

3. Analyzing Ligand Binding to Different Protein Conformations or Isoforms

Scenario: A protein exists in different states (e.g., active/inactive) or as different isoforms, and you have structures of a ligand bound to these variants.

How juProt Helps: Compare ProteinState1+Ligand with ProteinState2+Ligand. juProt can reveal how protein structural changes influence the interaction profile with a common ligand.

4. Validating Docking Poses

Scenario: You have multiple potential binding poses for a ligand from molecular docking.

How juProt Helps: Compare the interaction profile of different docked poses or a docked pose against an experimental structure (if available) to assess consistency.

5. Educational Purposes

Scenario: Teaching students about protein-ligand interactions.

How juProt Helps: Provides an easy-to-use tool for students to explore differential interactions without complex software or scripting.

Future Enhancements

juProt is an actively developed open-source project. Future versions aim to include:

• Enhanced visualization options, potentially including 2D comparative interaction diagrams.
• Allowing analysis of more than two complexes.
• User-configurable parameters for interaction detection.