Using Piper and Desmond for protein-protein interaction analysis involves several steps, from docking to molecular dynamics simulations. Here’s a brief overview of the process and some insights that might help you troubleshoot the lack of expected residue interactions in Desmond’s MD simulation:

1. Protein Preparation:

• Ensure that both proteins are properly prepared before docking. This includes protonation, assigning correct bond orders, and adding missing hydrogens.

2. Docking with Piper:

• Setup: Define the receptor and ligand (or in this case, the two proteins interacting).
• Docking: Run the docking protocol in Piper. You may want to explore different docking strategies and scoring functions to optimize the pose.
• Analysis: After docking, analyze the results to select the best pose(s) based on the docking score and any other criteria you have.

3. Preparing for MD with Desmond:

• Setup: Import the docked complex into Desmond. Ensure the complex is correctly oriented and that any necessary counterions are added for charge neutrality.
• System Building: Build the solvent environment around the complex, and then parameterize the system with the appropriate force field.
• Energy Minimization: Perform energy minimization to remove any steric clashes or high-energy conformations that may have arisen during the setup.

4. MD Simulation:

• Equilibration: Run an equilibration phase to allow the system to relax into a stable state. This usually involves gradually heating the system and then applying pressure restraints.
• Production Run: Conduct the production MD simulation under the desired conditions (temperature, pressure, etc.).

5. Analysis:

• Trajectory Analysis: After the simulation, analyze the trajectory to identify and characterize protein-protein interactions.

Insights for Expected Residue Interactions:

If you’re not seeing the expected residue interactions, consider the following:

• Docking Pose: Ensure the docking pose is accurate. Sometimes, the top scoring pose from docking may not represent the biologically relevant conformation. Try analyzing multiple top poses.
• Force Field and Parameters: Check that the force field and parameters used in Desmond are appropriate for the system you’re studying. Mismatches can lead to incorrect behavior.
• Simulation Time: The MD simulation might not have run long enough to observe the expected interactions. Proteins can take time to relax into their interacting conformations.
• Analysis Method: Make sure you’re using the correct method to analyze the MD trajectory. For protein-protein interactions, this might involve calculating distances, angles, hydrogen bonds, or other interaction types.
• Trajectory Sampling: The simulation might not be sampling the relevant regions of conformational space. You may need to run longer simulations or use enhanced sampling methods.
• Starting Structure: The structure you started with might have had some intrinsic strain or wasn’t the most stable form of the complex. Re-evaluate the starting structure if necessary.

Troubleshooting Steps:

If after these checks you still do not see the expected interactions, it may be necessary to revisit the experimental data supporting those expected interactions or consider additional computational or experimental approaches to validate your findings.

• Surely PIPER is an FFT-based protein docking program, so it is less accurate for docking antibody-protein antigen pairs and some similar docking structures, try HADDOCK as it uses flexible approaches to examine a wide range of conformations, making it effective in predicting binding poses and defining high-affinity complex structures, or you can go for NovaDock it utilizes best algorithm(SwarmDock) to predict protein-protein docking interactions. Hope this is helpful.

Rolando Garcia Hey.. I see that you are studying protein-protein interactions. I have a question - if 2 proteins, X and Y are binding and one of the proteins, X is NAD+ dependent, i.e. this protein functions with the help of NAD+, then while docking should I dock X-NAD+ complex with Y or just X and Y?