SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks

Bioinformatics
Manaz KaleelCatherine Mooney

Abstract

The subcellular location of a protein can provide useful information for protein function prediction and drug design. Experimentally determining the subcellular location of a protein is an expensive and time-consuming task. Therefore, various computer-based tools have been developed, mostly using machine learning algorithms, to predict the subcellular location of proteins. Here, we present a neural network based algorithm for protein subcellular location prediction. We introduce SCLpred-EMS a subcellular localization predictor powered by an ensemble of Deep N-to-1 Convolutional Neural Networks. SCLpred-EMS predicts the subcellular location of a protein into two classes, the endomembrane system and secretory pathway versus all others, with an MCC of 0.75-0.86 outperforming the other state-of-the-art web servers we tested. SCLpred-EMS is freely available for academic users at http://distilldeep.ucd.ie/SCLpred2/. Supplementary data are available at Bioinformatics online.

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 2, 2000·Nature Biotechnology·B SchwikowskiS Fields
Jun 6, 2006·Proteins·Chin-Sheng YuJenn-Kang Hwang
Jul 29, 2006·Bioinformatics·Andrea PierleoniRita Casadio
Jan 1, 2010·Nature Reviews. Drug Discovery·Lawrence RajendranKai Simons
Mar 4, 2011·Bioinformatics·Andrea PierleoniRita Casadio
May 6, 2011·Nucleic Acids Research·Andrea PierleoniRita Casadio
Sep 11, 2012·Bioinformatics·Tatyana GoldbergBurkhard Rost
Apr 10, 2013·Amino Acids·Catherine MooneyGianluca Pollastri
May 23, 2014·Nucleic Acids Research·Tatyana GoldbergBurkhard Rost
Oct 17, 2017·Bioinformatics·José Juan Almagro ArmenterosOle Winther
Dec 28, 2017·Bioinformatics·Castrense SavojardoRita Casadio
May 3, 2018·Nucleic Acids Research·Castrense SavojardoRita Casadio
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Feb 20, 2019·Nature Biotechnology·José Juan Almagro ArmenterosHenrik Nielsen
Aug 8, 2019·Amino Acids·Manaz KaleelGianluca Pollastri

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Citations

Dec 16, 2020·Scientific Reports·Jaesung OhRanjan Swarup
Dec 18, 2020·Life·Ravindra Kumar, Sandeep Kumar Dhanda
May 29, 2021·Frontiers in Microbiology·Padhmanand SudhakarSéverine Vermeire
Aug 17, 2021·Briefings in Bioinformatics·Patrick Brendan Timmons, Chandralal M Hewage

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