1. Prediction of peptidyl prolyl residues in cis/trans configuration using machine learning algorithms Jae-Hyung Lee Genetics, Development and Cell Biology Bioinformatics and Computational Biology Program
4. Torsional angles Although the peptide bond is planer and fixed rotation can and does occur about the two single bonds on either side of the a carbon: Φ (Phi), the bond between N and Ca Ψ (Psi), the bond between Ca and C
5. Two different peptide configurations cis ω = -20° ~ 20° trans ω = -180° ~ -160° or ω = 160° ~ 180°
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14. Result – Naïve Bayes Classifier (1) 0.230 0.610 0.201 0.602 21 0.229 0.609 0.199 0.601 19 0.235 0.610 0.202 0.602 17 0.245 0.614 0.209 0.606 15 0.254 0.618 0.194 0.598 13 0.270 0.625 0.201 0.602 11 0.282 0.629 0.210 0.606 9 0.302 0.637 0.195 0.599 7 0.296 0.635 0.204 0.604 5 0.276 0.628 0.190 0.596 3 CC Accuracy CC Accuracy window size ss information no ss information
15. Result – Naïve Bayes Classifier (2) No ss information ss information incorporated
16. Result – SVM (1) Polynomial kernel – third degree 0.3258 0.6634 0.2053 0.6037 21 0.3289 0.6649 0.2027 0.6028 19 0.3399 0.6704 0.1966 0.6001 17 0.3312 0.6662 0.1821 0.593 15 0.3253 0.6631 0.2059 0.6047 13 0.3192 0.66 0.2036 0.6034 11 0.3021 0.6515 0.1815 0.5921 9 0.305 0.653 0.1613 0.5817 7 0.246 0.6233 0.1499 0.575 5 0.2594 0.63 0.1625 0.5826 3 CC Accuracy CC Accuracy window size ss information no ss information
17. Result – SVM (2) No ss information ss information incorporated Polynomial kernel – third degree
18. Result – SVM (3) Window size 17 and ss information incorporated
