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Related Concept Videos

Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.

Ryota Ashizawa1,2,3,4, Sergei Kotelnikov1,2,4, Omeir Khan5

  • 1Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.

Proteins
|October 20, 2025
PubMed
Summary

Hybrid computational methods combining physics-based sampling and AI refinement significantly improve protein complex structure prediction accuracy. This approach enhances both protein-protein and protein-ligand docking, outperforming AI alone in challenging cases.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Artificial Intelligence in Biochemistry

Background:

  • Accurate prediction of protein complex structures is crucial for understanding biological functions.
  • Existing methods, including deep learning approaches like AlphaFold, have limitations in certain complex prediction scenarios.

Purpose of the Study:

  • To develop and evaluate hybrid computational strategies for enhanced protein-protein and protein-ligand complex structure prediction.
  • To demonstrate the synergistic benefits of combining physics-based modeling with AI-driven refinement.

Main Methods:

  • Protein-protein docking: Integrated physics-based sampling (ClusPro FFT, molecular dynamics) with AlphaFold (AF)-based sampling and refinement.
  • Protein-ligand docking: Combined template-based modeling (ClusPro LigTBM) with machine learning rescoring, physics-based local resampling, and diffusion models.

Main Results:

  • The hybrid protein-protein docking method generated high-accuracy models, succeeding in cases where AF alone failed.
  • The protein-ligand docking strategy achieved a competitive mean lDDT-PLI of 0.69 across 233 targets.
  • The integration of physics-based sampling and AI refinement proved critical for improving prediction accuracy.

Conclusions:

  • Hybrid computational approaches combining physics-based modeling and AI-driven refinement significantly enhance the accuracy of protein complex structure prediction.
  • These integrated strategies offer a powerful framework for tackling challenging protein-protein and protein-ligand docking problems.
  • The study highlights the importance of physics-based sampling in conjunction with deep learning for robust structural predictions.