Protein-protein interface simulation

Introduction

The PPI package aims to identify possible binding sites for a small molecule to inhibits the interface between two proteins.

Check out one of our related papers: Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose.

Inputs

  • protein-protein PDB file

  • ligand PDB file

  • input.yaml with parameters

Default parameters

The simulation consists of two stages: local exploration around the protein-protein interface and binding pose refinement.

Parameters for interface exploration:

  • iterations: 1

  • pele steps: 1000

Parameters for pose refinement:

  • iterations: 20

  • pele_steps: 12

Recommendations

  1. We recommend tracking the distance between a ligand atom and the center of interface to aid analysis of the simulation.

  2. There is no need to align the ligand, it will be automatically placed all around the protein interface by our automatic pipeline.

  3. We suggest using at least 50 CPUs.

  4. Expected computational time is around 9h.

1. Complex Preparation

Protein-protein file

The PDB file needs to be preprocessed with Maestro Protein Preparation Wizard. We usually recommend protonating the protein (obligatory), deleting water molecules more than 5Å away from ligands and ions as well as filling in missing loops and side chains.

Ligand file

The ligand needs to be correctly protonated, have unique chain ID and PDB atom names. It can have any residue name except for UNK.

2. Input Preparation

Prepare the input file input.yml as show in the template below:

system: '3d9u_prep.pdb' # protein-protein pdb
protein: 'A' # chain of the protein to keep
ligand_pdb: "3d9u_ligand.pdb" # ligand PDB file
chain: 'Z' # chain ID of the ligand
resname: 'LIG' # residue name of the ligand
center_of_interface: "A:306:O" # center of the protein-protein interface (chain ID:residue number:atom name)
seed: 12345
cpus: 50
# Distance to track along the simulation
atom_dist:
- "A:2:CA" # First atom to make the distance to
- "B:3:CG" # Second atom to make the distance to
ppi: true

For more optional flags please refer to optional flags.

3. Run simulation

Launch the simulation with the following command:

python -m pele_platform.main input.yml

4. Output

Main folders

The working directory will contain three folders:

  • 1_interface_exploration containing inputs and outputs of the initial induced fit simulation

  • 2_refinement_simulation containing inputs and outputs of the rescoring simulation

  • refinement_input with refinement simulation inputs, i.e. best energy cluster representatives from the interface exploration.

Raw output

Trajectory and report files for each simulation are located in working_folder/*/output/*. That’s where you can find detailed information on each snapshot (PDB file, binding energy, metrics, etc.).

Selected poses

Clusters

Upon completion of the refinement simulation, all trajectories are clustered based on ligand heavy atom coordinates. Then, a cluster representative with the best binding energy (or metric of your choice) is selected. Ranked cluster representatives can be found in:

working_folder/2_refinement_simulation/results/clusters

Best snapshots

In addition, top 100 structures with the best binding energy (or metric of your choice) are retrieved. This is done to ensure the clustering algorithm did not skip any valuable results. They are stored in:

working_folder/2_refinement_simulation/results/top_poses/