Related Experiment Video
Updated: May 28, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Evaluation of model quality predictions in CASP9.
Andriy Kryshtafovych1, Krzysztof Fidelis, Anna Tramontano
1Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA. akryshtafovych@ucdavis.edu
Proteins
|October 15, 2011
Summary
Protein structure prediction accuracy estimation has advanced significantly, with top methods nearing perfection. However, consensus approaches have limitations, and per-residue accuracy needs improvement.
Area of Science:
- Computational Biology
- Structural Biology
- Bioinformatics
Background:
- The Critical Assessment of protein Structure Prediction (CASP) has driven progress in estimating protein model accuracy since 2006.
- The inclusion of a model quality assessment category in CASP has spurred rapid development of new methods.
Purpose of the Study:
- To assess the state-of-the-art in a priori protein structure prediction accuracy estimation.
- To evaluate the performance of 46 quality assessment groups in predicting global and per-residue model accuracy.
Main Methods:
- Assessed method performance based on the correlation between predicted and observed model quality (global and local scales).
- Analyzed the ability of methods to identify the best models, differentiate good from bad models, and pinpoint well-modeled regions.
Main Results:
- Top global quality assessment methods achieve high performance (Pearson's correlation coefficients up to 0.97), approaching a perfection point.
- Consensus approaches dominate top performance but have inherent limitations.
- Methods analyzing individual models lag behind clustering techniques.
- Per-residue accuracy estimation methods are less accurate than global methods (correlation coefficients 0.63-0.72 for top groups).
Conclusions:
- While global quality assessment is nearing perfection, improvements are needed, particularly in addressing limitations of consensus approaches.
- Individual model analysis methods require significant enhancement.
- Further development is necessary to improve the accuracy of per-residue quality estimation in protein structure prediction.
More Related Videos
Related Concept Videos
01:29Protein Folding Quality Check in the RER
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...