Regression applied to protein binding site prediction and comparison with classification.
BACKGROUND
The structural genomics centers provide hundreds of protein structures of unknown function. Therefore, developing methods enabling the determination of a protein function automatically is imperative. The determination of a protein function can be achieved by studying the network of its physical interactions. In this context, identifying a potential binding site between proteins is of primary interest. In the literature, methods for predicting a potential binding site location generally are based on classification tools. The aim of this paper is to show that regression tools are more efficient than classification tools for patches based binding site predictors. For this purpose, we developed a patches based binding site localization method usable with either regression or classification tools.


RESULTS
We compared predictive performances of regression tools with performances of machine learning classifiers. Using leave-one-out cross-validation, we showed that regression tools provide better predictions than classification ones. Among regression tools, Multilayer Perceptron ranked highest in the quality of predictions. We compared also the predictive performance of our patches based method using Multilayer Perceptron with the performance of three other methods usable through a web server. Our method performed similarly to the other methods.


CONCLUSIONS
Regression is more efficient than classification when applied to our binding site localization method. When it is possible, using regression instead of classification for other existing binding site predictors will probably improve results. Furthermore, the method presented in this work is flexible because the size of the predicted binding site is adjustable. This adaptability is useful when either false positive or negative rates have to be limited.
Giard
Joachim
J
Communications and Remote Sensing Laboratory, Université Catholique de Louvain, Place du Levant 2, 1348 Louvain-la-Neuve, Belgium. joachim.giard@uclouvain.be
Ambroise
Jérôme
J
Gala
Jean-Luc
JL
Macq
Benoît
B
D000465:Algorithms; D001665:Binding Sites; D002965:Classification / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D012044:Regression Analysis
D011506:Proteins