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Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning
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DOI：10.1109/TCBB.2016.2602269.png)
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摘要
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The function of a protein is determined by its structure, which creates a need for efficient methods of protein structure determination to advance scientific and medical research. Because current experimental structure determination methods carry a high price tag, computational predictions are highly desirable. Given a protein sequence, computational methods produce numerous 3D structures known as decoys. Selection of the best quality decoys is both challenging and essential as the end users can handle only a few ones. Therefore, scoring functions are central to decoy selection. They combine measurable features into a single number indicator of decoy quality. Unfortunately, current scoring functions do not consistently select the best decoys. Machine learning techniques offer great potential to improve decoy scoring. This paper presents two machine-learning based scoring functions to predict the quality of proteins structures, i.e., the similarity between the predicted structure and the experimental one without knowing the latter. We use different metrics to compare these scoring functions against three state-of-the-art scores. This is a first attempt at comparing different scoring functions using the same non-redundant dataset for training and testing and the same features. The results show that adding informative features may be more significant than the method used.
Keyword:
Proteins
Training
Support vector machines
Amino acids
Electronic mail
Feature extraction
Machine learning algorithms
Algorithms
performance
machine learning
ensemble learning
Protein structure prediction
scoring functions
decoy quality assessment
protein features
machine learning
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3.4
论文数:
3.3K
被引数:
6.4K
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Scoring function for automated assessment of protein structure template quality用于自动评估蛋白质结构模板质量的评分功能
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分享收藏GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction.png)
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