Predicting lysine-malonylation sites of proteins using sequence and predicted structural features

Journal of Computational Chemistry
Ghazaleh TaherzadehYaoqi Zhou

Abstract

Malonylation is a recently discovered post-translational modification (PTM) in which a malonyl group attaches to a lysine (K) amino acid residue of a protein. In this work, a novel machine learning model, SPRINT-Mal, is developed to predict malonylation sites by employing sequence and predicted structural features. Evolutionary information and physicochemical properties are found to be the two most discriminative features whereas a structural feature called half-sphere exposure provides additional improvement to the prediction performance. SPRINT-Mal trained on mouse data yields robust performance for 10-fold cross validation and independent test set with Area Under the Curve (AUC) values of 0.74 and 0.76 and Matthews' Correlation Coefficient (MCC) of 0.213 and 0.20, respectively. Moreover, SPRINT-Mal achieved comparable performance when testing on H. sapiens proteins without species-specific training but not in bacterium S. erythraea. This suggests similar underlying physicochemical mechanisms between mouse and human but not between mouse and bacterium. SPRINT-Mal is freely available as an online server at: http://sparks-lab.org/server/SPRINT-Mal/. © 2018 Wiley Periodicals, Inc.

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Citations

Dec 24, 2018·Briefings in Functional Genomics·Wenying HeQuan Zou
Dec 14, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Abdollah DehzangiTatsuhiko Tsunoda
Apr 24, 2020·Computational and Structural Biotechnology Journal·Hussam Al-BarakatiDukka Kc
Oct 7, 2020·Computers in Biology and Medicine·Shubhashis Roy DiptaAbdollah Dehzangi

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