NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes

Bioinformatics
Dan Ofer, Michal Linial

Abstract

The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short functionally related NPs. Herein, we describe Neuropeptide Precursor Identifier (NeuroPID), a machine learning scheme that predicts metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational-statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89-94% accuracy and 90-93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-lik...Continue Reading

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Citations

May 6, 2014·Nucleic Acids Research·Solange KarsentyMichal Linial
Jul 2, 2015·Bioinformatics·Dan Ofer, Michal Linial
Jun 14, 2015·Annual Review of Analytical Chemistry·Amanda BuchbergerLingjun Li
Jul 15, 2016·Journal of Bioinformatics and Computational Biology·Liqi LiHua Yang
Nov 17, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Liqi LiHua Yang
Oct 4, 2016·Database : the Journal of Biological Databases and Curation·Nadav BrandesMichal Linial
Nov 8, 2017·Toxins·Michal LinialDan Ofer
Mar 12, 2018·Interdisciplinary Sciences, Computational Life Sciences·Juanjuan KangJian Huang
Mar 28, 2019·Scientific Reports·Piyush AgrawalIndrakant K Singh
Apr 27, 2021·Computational and Structural Biotechnology Journal·Dan OferMichal Linial
Sep 25, 2021·Mass Spectrometry Reviews·Ashley PhetsanthadLingjun Li

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