Prediction of peptide bonding affinity: kernel methods for nonlinear modeling

This paper presents regression models obtained from a process of blind prediction of peptide binding affinity from provided descriptors for several distinct datasets as part of the 2006 Comparative Evaluation of Prediction Algorithms (COEPRA) contest. This paper finds that kernel partial least squares, a nonlinear partial least squares (PLS) algorithm, outperforms PLS, and that the incorporation of transferable atom equivalent features improves predictive capability.