- if your pdb files contain more than one instance of your protein in the asymmetric unit, you may want to remove the additional copies

- downstreams processing will encounter fewer problems if, from the start, you ensure that the two proteins you are docking use different chain labels

- you may need to replace modified residues or non-standard residues by their non-modified counterpart (e.g. phosphorylations)

To achieve protein-protein interaction by molecular docking, you must first create the 3D structures of both the ligand (molecule) and the receptor (protein).

Ascertain if both structures are in a compatible format, often PDB. Predict the binding orientation and affinity between the ligand and receptor using molecular docking software such as AutoDock, AutoDock Vina, or Cluspro.

Upload your receptor and ligand PDB files if utilising the Cluspro service.

Analyse the results after post-docking to identify probable binding sites and interaction residues.

For accuracy, it is critical to validate predicted interactions using experimental approaches.

To achieve protein-protein interaction through molecular docking, the following steps are involved:

1.Preparation: Prepare the protein structures to be docked by removing water molecules, adding any missing atoms, and optimizing the structures.

2.Selection of Docking Software: Choose appropriate molecular docking software or tools that utilize algorithms to predict the best possible binding conformations between the proteins.

3.Docking Algorithm: Apply the selected docking algorithm, often based on scoring functions and search algorithms. These algorithms explore the possible orientations of the proteins and evaluate their compatibility based on various criteria, such as shape complementarity, electrostatic interactions, and hydrogen bonding.

4.Binding Site Identification: Identify the binding sites or regions on the proteins where interaction is likely to occur. These sites can be determined through experimental data, protein structures, or predictive algorithms.

5.Docking Simulation: Run the docking simulation by allowing the proteins to move and explore different conformations to find the most energetically favorable or probable binding configuration.

6.Scoring and Analysis: Evaluate and score the generated docking poses to identify the most promising protein-protein interaction models. Higher scores typically indicate better binding affinity and stability.

7.Validation: Validate the predicted protein-protein interactions using experimental techniques like biochemical assays, mutagenesis studies, or structural analysis (e.g., X-ray crystallography, NMR) to confirm the accuracy of the predicted complexes.