Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Computer Science, Baker Center for Bioinformatics and Biological Statistics
Journal or Book Title
By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes and other machine learning algorithms we are able to distinguish between two classes of protein sequences: those folding to highly-designable conformations, or those folding to poorly- or non-designable conformations.
First, we generate all possible compact lattice conformations for the specified shape (a hexagon or a triangle) on the 2D triangular lattice. Then we generate all possible binary hydrophobic/polar (H/P) sequences and by using a specified energy function, thread them through all of these compact conformations. If for a given sequence the lowest energy is obtained for a particular lattice conformation we assume that this sequence folds to that conformation. Highly-designable conformations have many H/P sequences folding to them, while poorly-designable conformations have few or no H/P sequences. We classify sequences as folding to either highly – or poorly-designable conformations. We have randomly selected subsets of the sequences belonging to highly-designable and poorly-designable conformations and used them to train several different standard machine learning algorithms.
By using these machine learning algorithms with ten-fold cross-validation we are able to classify the two classes of sequences with high accuracy – in some cases exceeding 95%.
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Peto et al
Peto, Myron; Kloczkowski, Andrzej; Honavar, Vasant; and Jernigan, Robert L., "Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable" (2008). Biochemistry, Biophysics and Molecular Biology Publications. 160.