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Updated: May 27, 2025
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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Slice'N'Dice: maximizing the value of predicted models for structural biologists
Adam J Simpkin1, Luc G Elliot1, Agnel Praveen Joseph2
1Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
Acta Crystallographica. Section D, Structural Biology
|February 20, 2025
Summary
Structural biologists can now use predicted protein models for molecular replacement and cryo-electron microscopy (cryoEM) model fitting. Slice'N'Dice software addresses domain orientation differences, improving structure determination accuracy.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Next-generation modeling methods like AlphaFold2 enable the use of predicted protein structures.
- Predicted structures are increasingly utilized for molecular replacement (MR) and cryo-electron microscopy (cryoEM) model fitting.
- A key limitation is the discrepancy in domain-domain orientations between predicted models and experimental structures.
Purpose of the Study:
- To introduce Slice'N'Dice, a software package designed to overcome limitations in using predicted protein models for structure determination.
- To enable accurate structure solutions by addressing domain-domain orientation differences in predicted models.
Main Methods:
- Slice'N'Dice segments predicted models into distinct structural units.
- These slices are automatically placed using established tools like Phaser, MOLREP, or PowerFit.
- Slicing can leverage AlphaFold's predicted aligned error (PAE) or Cα-atom-based clustering algorithms for broad applicability.
Main Results:
- The software effectively addresses domain-domain orientation differences, a common issue with predicted models.
- Slice'N'Dice facilitates automated placement of structural units for MR and cryoEM model fitting.
- The tool's flexibility allows user-defined or automatic determination of the number of slices.
Conclusions:
- Slice'N'Dice enhances the utility of predicted protein models in structural biology workflows.
- The software improves the accuracy and efficiency of obtaining structure solutions via MR and cryoEM.
- Slice'N'Dice is integrated into CCP4 and CCP-EM software suites, making it accessible to researchers.
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