dc.contributor.author | Taherzadeh, Ghazaleh | |
dc.contributor.author | Yang, Yuedong | |
dc.contributor.author | Xu, Haodong | |
dc.contributor.author | Xue, Yu | |
dc.contributor.author | Liew, Alan Wee-Chung | |
dc.contributor.author | Zhou, Yaoqi | |
dc.date.accessioned | 2019-06-07T01:44:04Z | |
dc.date.available | 2019-06-07T01:44:04Z | |
dc.date.issued | 2018 | |
dc.identifier.issn | 0192-8651 | |
dc.identifier.doi | 10.1002/jcc.25353 | |
dc.identifier.uri | http://hdl.handle.net/10072/382167 | |
dc.description.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. | |
dc.description.peerreviewed | Yes | |
dc.language | English | |
dc.language.iso | eng | |
dc.publisher | John Wiley & Sons | |
dc.publisher.place | United States | |
dc.relation.ispartofpagefrom | 1757 | |
dc.relation.ispartofpageto | 1763 | |
dc.relation.ispartofissue | 22 | |
dc.relation.ispartofjournal | Journal of Computational Chemistry | |
dc.relation.ispartofvolume | 39 | |
dc.subject.fieldofresearch | Physical chemistry | |
dc.subject.fieldofresearch | Theoretical and computational chemistry | |
dc.subject.fieldofresearch | Theoretical and computational chemistry not elsewhere classified | |
dc.subject.fieldofresearch | Nanotechnology | |
dc.subject.fieldofresearchcode | 3406 | |
dc.subject.fieldofresearchcode | 3407 | |
dc.subject.fieldofresearchcode | 340799 | |
dc.subject.fieldofresearchcode | 4018 | |
dc.subject.keywords | Support vector machines | |
dc.subject.keywords | Lysine‐malonylation sites prediction | |
dc.subject.keywords | Post translational modification | |
dc.title | Predicting lysine-malonylation sites of proteins using sequence and predicted structural features | |
dc.type | Journal article | |
dc.type.description | C1 - Articles | |
dc.type.code | C - Journal Articles | |
gro.faculty | Griffith Sciences, School of Information and Communication Technology | |
gro.hasfulltext | No Full Text | |
gro.griffith.author | Liew, Alan Wee-Chung | |