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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16.

Jian Liu, Pawan Neupane, Jianlin Cheng

Biorxiv : the Preprint Server for Biology

|March 31, 2025

Summary

MULTICOM4 improves protein complex structure prediction by integrating AlphaFold2 and AlphaFold3 with advanced techniques. This system demonstrated top performance in the Critical Assessment of Techniques for Protein Structure Prediction (CASP16) for modeling protein multimers.

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Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Accurate prediction of single-chain protein structures is largely solved by tools like AlphaFold.
Predicting the structure of multi-chain protein complexes (multimers) remains a significant challenge in computational biology.

Purpose of the Study:

To develop and evaluate MULTICOM4, an advanced system for protein complex structure prediction.
To improve the accuracy of modeling protein-protein interactions and multimeric structures.

Main Methods:

Integration of AlphaFold2 and AlphaFold3 with novel in-house techniques.
Development of protein complex stoichiometry prediction methods.
Generation of diverse multiple sequence alignments (MSAs) using sequence and structure data.
Implementation of exception handling and deep learning-based model quality assessment.

Main Results:

MULTICOM4 achieved top performance in the Critical Assessment of Techniques for Protein Structure Prediction (CASP16).
In CASP16 Phase 0 (no stoichiometry info), MULTICOM predictors showed the best performance (avg. TM-score 0.752, DockQ 0.584).
In CASP16 Phase 1 (with stoichiometry info), MULTICOM_human ranked among top predictors (avg. TM-score 0.797, DockQ 0.558).

Conclusions:

Combining AlphaFold2 and AlphaFold3 with enhanced MSAs, quality assessment, and stoichiometry prediction significantly improves protein complex structure prediction.
MULTICOM4 represents a substantial advancement in modeling the structure of protein multimers.