MLACP: machine-learning-based prediction of anticancer peptides

// Balachandran Manavalan 1 , Shaherin Basith 2 , Tae Hwan Shin 1, 3 , Sun Choi 2 , Myeong Ok Kim 4 and Gwang Lee 1, 3 1 Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea 2 College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea 3 Institute of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea 4 Division of Life Science and Applied Life Science (BK21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, Republic of Korea Correspondence to: Gwang Lee, email: glee@ajou.ac.kr Keywords: anticancer peptides, hybrid model, machine-learning parameters, random forest, support vector machine Received: May 16, 2017 Accepted: July 13, 2017 Published: August 19, 2017 ABSTRACT Cancer is the second leading cause of death globally, and use of therapeutic peptides to target and kill cancer cells has received considerable attention in recent years. Identification of anticancer peptides (ACPs) through wet-lab experimentation is expensive and often time consuming; therefore, development of an efficient computational method is essential to identify potential ACP candidates prior to in vitro experimentation. In this study, we developed support vector machine- and random forest-based machine-learning methods for the prediction of ACPs using the features calculated from the amino acid sequence, including amino acid composition, dipeptide composition, atomic composition, and physicochemical properties. We trained our methods using the Tyagi-B dataset and determined the machine parameters by 10-fold cross-validation. Furthermore, we evaluated the performance of our methods on two benchmarking datasets, with our results showing that the random forest-based method outperformed the existing methods with an average accuracy and Matthews correlation coefficient value of 88.7% and 0.78, respectively. To assist the scientific community, we also developed a publicly accessible web server at www.thegleelab.org/MLACP.html .