AlphaFold-Multimer_PPI_MD

This repository contains the workflow, scripts, and analysis pipelines developed for conformational sampling of protein–protein complexes using a hybrid AlphaFold-Multimer + Molecular Dynamics (MD) approach. The project constitutes one subchapter of Jianmin Wang’s Ph.D. dissertation at Yonsei University.

Protein-Protein Complex Conformational Sampling via AlphaFold-Multimer and Molecular Dynamics

Protein-protein interactions play a critical role in various biological processes, and accurately predicting their conformations remains a challenging task. In this study, we explore the conformational sampling of protein-protein complexes using AlphaFold-Multimer and molecular dynamics (MD) simulations. AlphaFold-Multimer was employed to generate multiple structural models with different initialization seeds, MSA depths, and dropout layer activation to assess its conformational diversity. Additionally, MD simulations were conducted using the Amber24 package to investigate the dynamic nature and stability of AlphaFold-Multimer-generated structures. The results were evaluated using metrics such as DockQ and iRMSD, which provide insights into the quality and accuracy of the predicted conformations. Our findings demonstrate that integrating AlphaFold-Multimer conformational sampling with MD simulations enhances the understanding of protein-protein complex dynamics, offering a more comprehensive approach for structural characterization.

Requirements

• biopython

https://github.com/biopython/biopython

• Amber

https://ambermd.org

• MDAnalysis

https://www.mdanalysis.org/

• nglview

https://github.com/nglviewer/nglview

• pytraj

https://github.com/Amber-MD/pytraj

• mdtraj

https://github.com/mdtraj/mdtraj

Molecular dynamics

Crystal structure of the Skp1-FBG3 complex：3WSO

prpepare topology and coordinate files

pdb4amber -i A.pdb -o a.pdb -y -d

pdb4amber -i a.pdb -o inputA.pdb --reduce

pdb4amber -i B.pdb -o b.pdb -y -d

pdb4amber -i b.pdb -o inputB.pdb --reduce


************tleap.in**********************************************
source leaprc.protein.ff14SB #Source leaprc file for ff14SB protein force field
source leaprc.water.tip3p #Source leaprc file for TIP3P water model

ProA = loadpdb inputA.pdb #Load A PDB file for protein
ProB = loadpdb inputB.pdb #Load B PDB file for protein

mol = combine {ProA,ProB}

check mol
solvatebox mol TIP3PBOX 12.0 #Solvate the complex with a cubic water box
addions mol Cl- 0 #Add Cl- ions to neutralize the system
addions mol Na+ 0 #Add Na+ ions to neutralize the system
charge mol
savepdb mol ppcomplex_solv.pdb
saveamberparm mol ppcomplex_solv.prmtop ppcomplex_solv.inpcrd #Save AMBER topology and coordinate files
quit #Quit tleap program
**********************************************************************

tleap -s -f tleap.in > tleap.out

Run molecular dynamics

Model Metrics

DockQ

DockQ: A Quality Measure for Protein-Protein Docking Models

https://github.com/bjornwallner/DockQ

• Basu, S. and Wallner, B., 2016. DockQ: a quality measure for protein-protein docking models. PloS one, 11(8), p.e0161879.
• Mirabello, Claudio, and Björn Wallner. "DockQ v2: Improved automatic quality measure for protein multimers, nucleic acids, and small molecules." Bioinformatics 40.10 (2024): btae586.

Conformational ensembles comparison: MD VS AlphaFold-Multimer

License

Code is released under GNU GENERAL PUBLIC LICENSE.

Cite:

• Wang, J. (2025). Protein-Protein Complex Conformational Sampling via AlphaFold-Multimer and Molecular Dynamics [Zenodo]. https://doi.org/10.5281/zenodo.17854345
• Jianmin Wang, Xun Wang, Yanyi Chu, Chunyan Li, Xue Li, Xiangyu Meng, Yitian Fang, Kyoung Tai No, Jiashun Mao, Xiangxiang Zeng. "Exploring the conformational ensembles of protein-protein complex with transformer-based generative model." Journal of Chemical Theory and Computation; doi: https://doi.org/10.1021/acs.jctc.4c00255

Note

https://ambermd.org

https://github.com/sokrypton/ColabFold

https://github.com/steineggerlab/colabfold-protocol