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Updated: May 10, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2
Liam J McGuffin1, Shaima N Alhaddad1, Behnosh Behzadi1
1School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6DH, United Kingdom.
Predicting protein complex structures is crucial. MultiFOLD2 and ModFOLDdock2 are advanced tools for protein quaternary structure prediction and quality assessment, showing top performance in recent benchmarks.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Understanding protein complex structures is vital for advancements in medicine, agriculture, and bioengineering.
- Accurate prediction and quality assessment of these structures are key challenges in the field.
Purpose of the Study:
- To introduce and describe the MultiFOLD2 and ModFOLDdock2 computational servers.
- To highlight their capabilities in protein quaternary structure prediction and model quality assessment.
Main Methods:
- MultiFOLD2: Integrated stoichiometry prediction, enhanced sampling, and scoring for quaternary structure prediction.
- ModFOLDdock2: Hybrid consensus approach for global and local quality scoring of predicted quaternary structures.
Main Results:
- MultiFOLD2 demonstrates high performance in benchmarks like CAMEO.
- ModFOLDdock2 provides reliable quality scores and integrates with MultiFOLD2.
- Both servers ranked highly in the CASP16 experiment for their respective categories.
Conclusions:
- MultiFOLD2 and ModFOLDdock2 are leading, rigorously evaluated servers for protein quaternary structure prediction and quality assessment.
- These freely accessible web servers offer user-friendly interfaces for researchers worldwide.
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