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Biological function derived from predicted structures in CASP11.

Peter J Huwe¹, Qifang Xu¹, Maxim V Shapovalov¹

¹Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111.

|May 17, 2016

Summary

This summary is machine-generated.

This study evaluated protein structure models for biological function tasks in CASP11. While models showed some success in predicting protein-protein interactions and mutation effects, their accuracy varied significantly, limiting their direct biological application.

Keywords:

CASP11 missense mutation phenotype prediction protein docking protein function protein structure prediction

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Area of Science:

Computational Biology
Structural Bioinformatics
Protein Structure Prediction

Background:

The CASP11 (Critical Assessment of protein Structure Prediction) experiment aimed to assess the biological relevance of predicted protein structures.
Evaluating predicted structures based on their ability to perform quantifiable biological tasks is crucial for advancing structural bioinformatics.

Purpose of the Study:

To assess the utility of predicted protein models from CASP11 for biological inference.
To quantify the performance of predicted models in tasks including homodimer docking, ligand binding, and predicting mutation phenotypes.

Main Methods:

Assessed homodimer formation accuracy of predicted models as a function of monomer GDT-TS (Global Distance Test Total Score).
Performed ligand docking into predicted models and compared ligand RMSD (Root Mean Square Deviation) with experimental structures.
Evaluated the utility of models in predicting missense mutation phenotypes by comparing calculated features with experimental structures.

Main Results:

Homodimer docking accuracy improved with higher monomer GDT-TS, but success was inconsistent above 60% GDT-TS.
Ligand docking to predicted models yielded poor RMSD values, and contact similarity measures did not correlate well with model accuracy.
Models successfully reproduced accessible surface areas but showed limited correlation with FoldX energy changes for missense mutations.

Conclusions:

Predicted protein models show potential for biological inference, particularly in tasks like homodimer formation, but require further improvement for reliable application.
The accuracy of predicted structures is critical for their utility in downstream biological function assessments, including ligand binding and mutation effect prediction.