The Importance of the ProtDeform Score in Protein Structure Prediction
Author Information
Author(s): Jairo Rocha, Ricardo Alberich, Peter Csermely
Primary Institution: University of the Balearic Islands
Hypothesis
The ProtDeform score can provide objective reasons for preferring one protein aligner over another.
Conclusion
PD-scores are at least as valuable for prediction scoring as TM-scores and are even more reliable for protein classification.
Supporting Evidence
- PD-scores are length independent and follow an Extreme Value Distribution.
- PD-scores and TM-scores are highly correlated with a Spearman coefficient of 0.95.
- Around 20% of CASP8 predictions have scores that do not reach the significant P-value threshold.
Takeaway
This study shows that a new scoring system for protein alignment can help scientists better understand how similar two proteins are.
Methodology
The study analyzed the ProtDeform score and compared it with TM-scores using various benchmarks for protein classification.
Potential Biases
Potential biases in the selection of protein structures for benchmarking.
Limitations
The study may not account for all possible protein structures and their variations.
Participant Demographics
The study involved protein structures from the CASP8 predictions.
Statistical Information
P-Value
0.0018
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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