Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.

BMC Bioinformatics
Rasna R WaliaVasant Honavar

Abstract

RNA molecules play diverse functional and structural roles in cells. They function as messengers for transferring genetic information from DNA to proteins, as the primary genetic material in many viruses, as catalysts (ribozymes) important for protein synthesis and RNA processing, and as essential and ubiquitous regulators of gene expression in living organisms. Many of these functions depend on precisely orchestrated interactions between RNA molecules and specific proteins in cells. Understanding the molecular mechanisms by which proteins recognize and bind RNA is essential for comprehending the functional implications of these interactions, but the recognition 'code' that mediates interactions between proteins and RNA is not yet understood. Success in deciphering this code would dramatically impact the development of new therapeutic strategies for intervening in devastating diseases such as AIDS and cancer. Because of the high cost of experimental determination of protein-RNA interfaces, there is an increasing reliance on statistical machine learning methods for training predictors of RNA-binding residues in proteins. However, because of differences in the choice of datasets, performance measures, and data representations use...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 13, 2001·Nucleic Acids Research·S JonesJ M Thornton
Jul 27, 2001·Journal of Molecular Biology·J Allers, Y Shamoo
Aug 14, 2001·Journal of Molecular Recognition : JMR·M Treger, E Westhof
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Iddo Friedberg, Hanah Margalit
Feb 13, 2002·Current Opinion in Structural Biology·Olivier Lichtarge, Mathew E Sowa
May 9, 2002·Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme·Masami Kusunoki
May 31, 2002·Acta Crystallographica. Section D, Biological Crystallography·Helen M BermanChristine Zardecki
Feb 22, 2005·BMC Bioinformatics·Shandar Ahmad, Akinori Sarai
Mar 16, 2005·Proteins·Rafał AdamczakJarosław Meller
Aug 13, 2005·Bioinformatics·Tobias SingThomas Lengauer
Nov 30, 2005·Methods : a Companion to Methods in Enzymology·Jernej UleRobert B Darnell
Jun 23, 2006·RNA·Michael TerribiliniDrena Dobbs
Jul 18, 2006·Nucleic Acids Research·Liangjiang Wang, Susan J Brown
Dec 23, 2006·Proteins·Jonathan J EllisSusan Jones
May 8, 2007·Nucleic Acids Research·Michael TerribiliniDrena Dobbs
May 24, 2007·Bioinformatics·John A Capra, Mona Singh
Jul 25, 2007·Bioinformatics·Yanay OfranBurkhard Rost
Aug 19, 2007·Nature Protocols·Lance M Hellman, Michael G Fried
Oct 13, 2007·Proteins·Manish KumarG P S Raghava
Oct 19, 2007·Journal of Biomolecular Screening·Nicholas L MillsR Kiplin Guy
Oct 20, 2007·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Liangjiang Wang, Susan J Brown
Feb 12, 2008·Computer Methods and Programs in Biomedicine·Jing TongZu-Hong Lu
Aug 22, 2008·PLoS Computational Biology·Shula Shazman, Yael Mandel-Gutfreund
Jun 11, 2009·Protein and Peptide Letters·Quan LiHaiyan Liu
Aug 25, 2009·Computational Biology and Chemistry·Ruth V Spriggs, Susan Jones
Dec 19, 2009·Nature Reviews. Genetics·Donny D Licatalosi, Robert B Darnell
Mar 20, 2010·International Journal of Data Mining and Bioinformatics·Fadi TowficVasant Honavar
May 19, 2010·Nucleic Acids Research·Matthew B CarsonHui Lu
Jun 11, 2010·Annual Review of Biochemistry·Marc Robert FabianWitold Filipowicz

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Citations

May 22, 2013·Molecular and Cellular Biology·Priyanka DasBarsanjit Mazumder
Jul 27, 2014·Nucleic Acids Research·Songling LiDaron M Standley
Nov 6, 2015·International Journal of Molecular Sciences·Jingna SiRongling Wu
Mar 19, 2014·The Plant Journal : for Cell and Molecular Biology·Jie QuJyan-Chyun Jang
Jun 26, 2015·Nucleic Acids Research·Zhenling Peng, Lukasz Kurgan
Oct 3, 2013·Methods : a Companion to Methods in Enzymology·Irina TuszynskaJanusz M Bujnicki
Jul 8, 2016·PloS One·Yasser El-ManzalawyVasant Honavar
Nov 7, 2016·Methods : a Companion to Methods in Enzymology·Laura Pérez-CanoJuan Fernández-Recio
Dec 21, 2016·Bioinformatics·Xiaoli Zhang, Shiyong Liu
Mar 10, 2016·PloS One·Juliana Ramos Martins, Márcia Maria Gentile Bitondi
Dec 9, 2017·BMC Bioinformatics·Yongjun TangLei Deng
Mar 24, 2017·Briefings in Bioinformatics·Jian Zhang, Lukasz Kurgan
Jul 23, 2013·Molecular BioSystems·Huiying ZhaoYaoqi Zhou
May 31, 2018·International Journal of Molecular Sciences·Ambuj SrivastavaM Michael Gromiha
Sep 24, 2020·International Journal of Molecular Sciences·Kui WangLukasz Kurgan
Jan 15, 2021·Journal of Molecular Recognition : JMR·Yang LiuChunhua Li
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan

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Datasets Mentioned

BETA
RB198Seq
RB198

Methods Mentioned

BETA
X-ray
NMR
PSSMSeq
RB144Seq
RB106Seq
pulls down

Software Mentioned

IDSeq
ROCR
PRINTR
BLAST
PiRaNhA
PSSMSeq
OPRA
Surface
Weka workbench
DRNA

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