Generic placeholder image

Protein & Peptide Letters


ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Review Article

Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions

Author(s): Amit Sagar and Bin Xue*

Volume 26, Issue 8, 2019

Page: [601 - 619] Pages: 19

DOI: 10.2174/0929866526666190619103853


The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to determine RNA-protein interactions in multiple aspects. However, due to the facts that RNA-protein interactions are tissuespecific and condition-specific, as well as these interactions are weak and frequently compete with each other, those experimental techniques can not be made full use of to discover the complete spectrum of RNA-protein interactions. To moderate these issues, continuous efforts have been devoted to developing high quality computational techniques to study the interactions between RNAs and proteins. Many important progresses have been achieved with the application of novel techniques and strategies, such as machine learning techniques. Especially, with the development and application of CLIP techniques, more and more experimental data on RNA-protein interaction under specific biological conditions are available. These CLIP data altogether provide a rich source for developing advanced machine learning predictors. In this review, recent progresses on computational predictors for RNA-protein interaction were summarized in the following aspects: dataset, prediction strategies, and input features. Possible future developments were also discussed at the end of the review.

Keywords: RNA-protein interaction, RNA-binding protein, RNA-binding domain, RNA-binding motif, RNA-binding residue, protein-binding nucleotide, machine learning, deep learning, meta-strategy, UniProt, PDB, CLIP, sequence feature, structural feature, physicochemical feature, evolutionary information, PSSM.

Jones, S. Protein-RNA interactions: Structural biology and computational modeling techniques. Biophys. Rev., 2016, 8(4), 359-367.
[] [PMID: 28510023]
Glisovic, T.; Bachorik, J.L.; Yong, J.; Dreyfuss, G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett., 2008, 582(14), 1977-1986.
[] [PMID: 18342629]
Cook, K.B.; Hughes, T.R.; Morris, Q.D. High-throughput characterization of protein-RNA interactions. Brief. Funct. Genomics, 2015, 14(1), 74-89.
[] [PMID: 25504152]
Castello, A.; Fischer, B.; Eichelbaum, K.; Horos, R.; Beckmann, B.M.; Strein, C.; Davey, N.E.; Humphreys, D.T.; Preiss, T.; Steinmetz, L.M.; Krijgsveld, J.; Hentze, M.W. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 2012, 149(6), 1393-1406.
[] [PMID: 22658674]
Turner, M.; Díaz-Muñoz, M.D. RNA-binding proteins control gene expression and cell fate in the immune system. Nat. Immunol., 2018, 19(2), 120-129.
[] [PMID: 29348497]
Stülke, J. Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures. Arch. Microbiol., 2002, 177(6), 433-440.
[] [PMID: 12029388]
Van Assche, E.; Van Puyvelde, S.; Vanderleyden, J.; Steenackers, H.P. RNA-binding proteins involved in post-transcriptional regulation in bacteria. Front. Microbiol., 2015, 6, 141.
[] [PMID: 25784899]
Pullmann, R., Jr; Kim, H.H.; Abdelmohsen, K.; Lal, A.; Martindale, J.L.; Yang, X.; Gorospe, M. Analysis of turnover and translation regulatory RNA-binding protein expression through binding to cognate mRNAs. Mol. Cell. Biol., 2007, 27(18), 6265-6278.
[] [PMID: 17620417]
Marchese, D.; de Groot, N.S.; Lorenzo Gotor, N.; Livi, C.M.; Tartaglia, G.G. Advances in the characterization of RNA-binding proteins. Wiley Interdiscip. Rev. RNA, 2016, 7(6), 793-810.
[] [PMID: 27503141]
Gilbertson, S.; Federspiel, J.D.; Hartenian, E.; Cristea, I.M.; Glaunsinger, B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. eLife, 2018, 7, 7.
[] [PMID: 30281021]
Rio, D.C. RNA binding proteins, splice site selection, and alternative pre-mRNA splicing. Gene Expr., 1992, 2(1), 1-5.
[PMID: 1617299]
Fu, X.D.; Ares, M. Jr Context-dependent control of alternative splicing by RNA-binding proteins. Nat. Rev. Genet., 2014, 15(10), 689-701.
[] [PMID: 25112293]
Dominguez, D.; Freese, P.; Alexis, M.S.; Su, A.; Hochman, M. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol. Cell, 2018, 70, 854-867.
Babitzke, P.; Baker, C.S.; Romeo, T. Regulation of translation initiation by RNA binding proteins. Annu. Rev. Microbiol., 2009, 63, 27-44.
[] [PMID: 19385727]
Re, A.; Waldron, L.; Quattrone, A. Control of gene expression by RNA binding protein action on alternative translation initiation sites. PLoS Comput. Biol., 2016, 12(12)e1005198
[] [PMID: 27923063]
Harvey, R.F.; Smith, T.S.; Mulroney, T.; Queiroz, R.M.L.; Pizzinga, M.; Dezi, V.; Villenueva, E.; Ramakrishna, M.; Lilley, K.S.; Willis, A.E. Trans-acting translational regulatory RNA binding proteins. Wiley Interdiscip. Rev. RNA, 2018, 9(3)e1465
[] [PMID: 29341429]
Dassi, E. Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins. Front. Mol. Biosci., 2017, 4, 67.
[] [PMID: 29034245]
Ambros, V. The functions of animal microRNAs. Nature, 2004, 431(7006), 350-355.
[] [PMID: 15372042]
Bartel, D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2), 281-297.
[] [PMID: 14744438]
Zealy, R.W.; Wrenn, S.P.; Davila, S.; Min, K.W.; Yoon, J.H. microRNA-binding proteins: Specificity and function. Wiley Interdiscip. Rev. RNA, 2017, 8(5), 8.
[] [PMID: 28130820]
Jiang, P.; Coller, H. Functional interactions between microRNAs and RNA binding proteins. MicroRNA, 2012, 1(1), 70-79.
[] [PMID: 25048093]
Nussbacher, J.K.; Yeo, G.W. Systematic discovery of RNA binding proteins that Regulate microRNA levels. Mol. Cell, 2018, 69, 1005-1016.
Treiber, T.; Treiber, N.; Plessmann, U.; Harlander, S.; Daiss, J.L. A Compendium of RNA-binding proteins that regulate microRNA biogenesis. Mol. Cell, 2017, 66, 270-284.
Ciafrè, S.A.; Galardi, S. microRNAs and RNA-binding proteins: A complex network of interactions and reciprocal regulations in cancer. RNA Biol., 2013, 10(6), 935-942.
[] [PMID: 23696003]
Wang, K.C.; Chang, H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell, 2011, 43(6), 904-914.
[] [PMID: 21925379]
Guttman, M.; Rinn, J.L. Modular regulatory principles of large non-coding RNAs. Nature, 2012, 482(7385), 339-346.
[] [PMID: 22337053]
Li, J.H.; Liu, S.; Zheng, L.L.; Wu, J.; Sun, W.J.; Wang, Z.L.; Zhou, H.; Qu, L.H.; Yang, J.H. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front. Bioeng. Biotechnol., 2015, 2, 88.
[] [PMID: 25642422]
Noh, J.H.; Kim, K.M.; McClusky, W.G.; Abdelmohsen, K.; Gorospe, M. Cytoplasmic functions of long noncoding RNAs. Wiley Interdiscip. Rev. RNA, 2018, 9(3)e1471
[] [PMID: 29516680]
Long, Y.; Wang, X.; Youmans, D.T.; Cech, T.R. How do lncRNAs regulate transcription? Sci. Adv., 2017, 3(9)eaao2110
[] [PMID: 28959731]
Quinodoz, S.; Guttman, M. Long noncoding RNAs: An emerging link between gene regulation and nuclear organization. Trends Cell Biol., 2014, 24(11), 651-663.
[] [PMID: 25441720]
Lukong, K.E.; Chang, K.W.; Khandjian, E.W.; Richard, S. RNA-binding proteins in human genetic disease. Trends Genet., 2008, 24(8), 416-425.
[] [PMID: 18597886]
Musunuru, K. Cell-specific RNA-binding proteins in human disease. Trends Cardiovasc. Med., 2003, 13(5), 188-195.
[] [PMID: 12837581]
Castello, A.; Fischer, B.; Hentze, M.W.; Preiss, T. RNA-binding proteins in Mendelian disease. Trends Genet., 2013, 29(5), 318-327.
[] [PMID: 23415593]
Zhou, H.; Mangelsdorf, M.; Liu, J.; Zhu, L.; Wu, J.Y. RNA-binding proteins in neurological diseases. Sci. China Life Sci., 2014, 57(4), 432-444.
[] [PMID: 24658850]
Brinegar, A.E.; Cooper, T.A. Roles for RNA-binding proteins in development and disease. Brain Res., 2016, 1647, 1-8.
[] [PMID: 26972534]
de Bruin, R.G.; Rabelink, T.J.; van Zonneveld, A.J.; van der Veer, E.P. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur. Heart J., 2017, 38(18), 1380-1388.
[] [PMID: 28064149]
Pérez-Boza, J.; Lion, M.; Struman, I. Exploring the RNA landscape of endothelial exosomes. RNA, 2018, 24(3), 423-435.
[] [PMID: 29282313]
Sork, H.; Corso, G.; Krjutskov, K.; Johansson, H.J.; Nordin, J.Z.; Wiklander, O.P.B.; Lee, Y.X.F.; Westholm, J.O.; Lehtiö, J.; Wood, M.J.A.; Mäger, I.; El Andaloussi, S. Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome. Sci. Rep., 2018, 8(1), 10813.
[] [PMID: 30018314]
Janas, T.; Janas, M.M.; Sapoń, K.; Janas, T. Mechanisms of RNA loading into exosomes. FEBS Lett., 2015, 589(13), 1391-1398.
[] [PMID: 25937124]
Statello, L.; Maugeri, M.; Garre, E.; Nawaz, M.; Wahlgren, J.; Papadimitriou, A.; Lundqvist, C.; Lindfors, L.; Collén, A.; Sunnerhagen, P.; Ragusa, M.; Purrello, M.; Di Pietro, C.; Tigue, N.; Valadi, H. Identification of RNA-binding proteins in exosomes capable of interacting with different types of RNA: RBP-facilitated transport of RNAs into exosomes. PLoS One, 2018, 13(4)e0195969
[] [PMID: 29689087]
Raposo, G.; Stoorvogel, W. Extracellular vesicles: exosomes, microvesicles, and friends. J. Cell Biol., 2013, 200(4), 373-383.
[] [PMID: 23420871]
Koga, S.; Williams, D.S.; Perriman, A.W.; Mann, S. Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model. Nat. Chem., 2011, 3(9), 720-724.
[] [PMID: 21860462]
Weber, S.C.; Brangwynne, C.P. Getting RNA and protein in phase. Cell, 2012, 149(6), 1188-1191.
[] [PMID: 22682242]
Hyman, A.A.; Weber, C.A.; Jülicher, F. Liquid-liquid phase separation in biology. Annu. Rev. Cell Dev. Biol., 2014, 30, 39-58.
[] [PMID: 25288112]
Water, J.J.; Schack, M.M.; Velazquez-Campoy, A.; Maltesen, M.J.; van de Weert, M.; Jorgensen, L. Complex coacervates of hyaluronic acid and lysozyme: Effect on protein structure and physical stability. Eur. J. Pharm. Biopharm., 2014, 88(2), 325-331.
[] [PMID: 25218319]
Jia, T.Z.; Hentrich, C.; Szostak, J.W. Rapid RNA exchange in aqueous two-phase system and coacervate droplets. Orig. Life Evol. Biosph., 2014, 44(1), 1-12.
[] [PMID: 24577897]
Antonov, M.; Mazzawi, M.; Dubin, P.L. Entering and exiting the protein-polyelectrolyte coacervate phase via nonmonotonic salt dependence of critical conditions. Biomacromolecules, 2010, 11(1), 51-59.
[] [PMID: 19947624]
Drobot, B.; Iglesias-Artola, J.M.; Le Vay, K.; Mayr, V.; Kar, M.; Kreysing, M.; Mutschler, H.; Tang, T.D. Compartmentalised RNA catalysis in membrane-free coacervate protocells. Nat. Commun., 2018, 9(1), 3643.
[] [PMID: 30194374]
Falahati, H.; Wieschaus, E. Independent active and thermodynamic processes govern the nucleolus assembly in vivo. Proc. Natl. Acad. Sci. USA, 2017, 114(6), 1335-1340.
[] [PMID: 28115706]
Sokolova, E.; Spruijt, E.; Hansen, M.M.; Dubuc, E.; Groen, J.; Chokkalingam, V.; Piruska, A.; Heus, H.A.; Huck, W.T. Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate. Proc. Natl. Acad. Sci. USA, 2013, 110(29), 11692-11697.
[] [PMID: 23818642]
Aumiller, W.M., Jr; Pir Cakmak, F.; Davis, B.W.; Keating, C.D. RNA-based coacervates as a model for membraneless organelles: Formation, properties, and interfacial liposome assembly. Langmuir, 2016, 32(39), 10042-10053.
[] [PMID: 27599198]
Poudyal, R.R.; Pir Cakmak, F.; Keating, C.D.; Bevilacqua, P.C. Physical principles and extant biology reveal roles for RNA-containing membraneless compartments in origins of life chemistry. Biochemistry, 2018, 57(17), 2509-2519.
[] [PMID: 29560725]
Lunde, B.M.; Moore, C.; Varani, G. RNA-binding proteins: Modular design for efficient function. Nat. Rev. Mol. Cell Biol., 2007, 8(6), 479-490.
[] [PMID: 17473849]
Mackereth, C.D.; Sattler, M. Dynamics in multi-domain protein recognition of RNA. Curr. Opin. Struct. Biol., 2012, 22(3), 287-296.
[] [PMID: 22516180]
Bruinsma, R.F.; Bruinsma, R.F. (2002) Physics of protein-DNA interaction. Phys. a-Stat. Mech. Its Appl., 2002(313), 211-237.
Šponer, J.; Krepl, M.; Banáš, P.; Kührová, P.; Zgarbová, M.; Jurečka, P.; Havrila, M.; Otyepka, M. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes? Wiley Interdiscip. Rev. RNA, 2017, 8(3), 8.
[] [PMID: 27863061]
Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R.A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P.; Walter, N.G.; Otyepka, M. RNA structural dynamics as captured by molecular simulations: A comprehensive overview. Chem. Rev., 2018, 118(8), 4177-4338.
[] [PMID: 29297679]
McDowell, S.E.; Spacková, N.; Sponer, J.; Walter, N.G. Molecular dynamics simulations of RNA: An in silico single molecule approach. Biopolymers, 2007, 85(2), 169-184.
[] [PMID: 17080418]
Bahadur, R.P.; Kannan, S.; Zacharias, M. Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations. Biophys. J., 2009, 97(12), 3139-3149.
[] [PMID: 20006951]
Estarellas, C.; Otyepka, M.; Koča, J.; Banáš, P.; Krepl, M.; Šponer, J. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim. Biophys. Acta, 2015, 1850(5), 1072-1090.
[] [PMID: 25450173]
Fulle, S.; Gohlke, H. Molecular recognition of RNA: Challenges for modelling interactions and plasticity. J. Mol. Recognit., 2010, 23(2), 220-231.
[PMID: 19941322]
Si, J.; Cui, J.; Cheng, J.; Wu, R. Computational prediction of RNA-Binding proteins and binding sites. Int. J. Mol. Sci., 2015, 16(11), 26303-26317.
[] [PMID: 26540053]
Puton, T.; Kozlowski, L.; Tuszynska, I.; Rother, K.; Bujnicki, J.M. Computational methods for prediction of protein-RNA interactions. J. Struct. Biol., 2012, 179(3), 261-268.
[] [PMID: 22019768]
Mandal, M.; Breaker, R.R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol., 2004, 5(6), 451-463.
[] [PMID: 15173824]
Murray, J.B.; Terwey, D.P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W.G. The structural basis of hammerhead ribozyme self-cleavage. Cell, 1998, 92(5), 665-673.
[] [PMID: 9506521]
Puglisi, J.D.; Tan, R.; Calnan, B.J.; Frankel, A.D.; Williamson, J.R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science, 1992, 257(5066), 76-80.
[] [PMID: 1621097]
Fourmy, D.; Yoshizawa, S.; Puglisi, J.D. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J. Mol. Biol., 1998, 277(2), 333-345.
[] [PMID: 9514734]
Faber, C.; Sticht, H.; Schweimer, K.; Rösch, P. Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B. J. Biol. Chem., 2000, 275(27), 20660-20666.
[] [PMID: 10747964]
Kuiper, E.G.; Conn, G.L. Binding induced RNA conformational changes control substrate recognition and catalysis by the thiostrepton resistance methyltransferase (Tsr). J. Biol. Chem., 2014, 289(38), 26189-26200.
[] [PMID: 25086036]
Jiang, F.; Zhou, K.; Ma, L.; Gressel, S.; Doudna, J.A. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science, 2015, 348(6242), 1477-1481.
[] [PMID: 26113724]
Shibata, T.; Fujita, Y.; Ohno, H.; Suzuki, Y.; Hayashi, K.; Komatsu, K.R.; Kawasaki, S.; Hidaka, K.; Yonehara, S.; Sugiyama, H.; Endo, M.; Saito, H. Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat. Commun., 2017, 8(1), 540.
[] [PMID: 28912471]
Salomon, W.E.; Jolly, S.M.; Moore, M.J.; Zamore, P.D.; Serebrov, V. Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. Cell, 2016, 166(2), 517-520.
[] [PMID: 28777949]
Flores, J.K.; Ataide, S.F. Structural changes of RNA in complex with proteins in the SRP. Front. Mol. Biosci., 2018, 5, 7.
[] [PMID: 29459899]
Malgieri, G.; Palmieri, M.; Russo, L.; Fattorusso, R.; Pedone, P.V.; Isernia, C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J., 2015, 282(23), 4480-4496.
[] [PMID: 26365095]
Fu, M.; Blackshear, P.J. RNA-binding proteins in immune regulation: A focus on CCCH zinc finger proteins. Nat. Rev. Immunol., 2017, 17(2), 130-143.
[] [PMID: 27990022]
Tompa, P.; Csermely, P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J., 2004, 18(11), 1169-1175.
[] [PMID: 15284216]
Draper, D.E. Themes in RNA-protein recognition. J. Mol. Biol., 1999, 293(2), 255-270.
[] [PMID: 10550207]
Cusack, S. RNA-protein complexes. Curr. Opin. Struct. Biol., 1999, 9(1), 66-73.
[] [PMID: 10400475]
Kligun, E.; Mandel-Gutfreund, Y. The role of RNA conformation in RNA-protein recognition. RNA Biol., 2015, 12(7), 720-727.
[] [PMID: 25932908]
Maris, C.; Dominguez, C.; Allain, F.H. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J., 2005, 272(9), 2118-2131.
[] [PMID: 15853797]
Xue, B.; Dunker, A.K.; Uversky, V.N. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J. Biomol. Struct. Dyn., 2012, 30(2), 137-149.
[] [PMID: 22702725]
Chowdhury, S.; Zhang, J.; Kurgan, L. In Silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome. Proteomics, 2018, 18(21-22)e1800064
[] [PMID: 29806170]
Bowie, J.U.; Lüthy, R.; Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 1991, 253(5016), 164-170.
[] [PMID: 1853201]
Jones, D.T.; Taylor, W.R.; Thornton, J.M. A new approach to protein fold recognition. Nature, 1992, 358(6381), 86-89.
[] [PMID: 1614539]
Redfern, O.C.; Dessailly, B.; Orengo, C.A. Exploring the structure and function paradigm. Curr. Opin. Struct. Biol., 2008, 18(3), 394-402.
[] [PMID: 18554899]
Shang, L.; Gardner, D.P.; Xu, W.; Cannone, J.J.; Miranker, D.P.; Ozer, S.; Gutell, R.R. Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems. BMC Syst. Biol., 2013, 7(Suppl. 4), S13.
[] [PMID: 24565058]
Fetrow, J.S.; Skolnick, J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol., 1998, 281(5), 949-968.
[] [PMID: 9719646]
Zheng, J.; Kundrotas, P.J.; Vakser, I.A.; Liu, S. Template-based modeling of protein-RNA interactions. PLoS Comput. Biol., 2016, 12(9)e1005120
[] [PMID: 27662342]
Yang, Y.; Zhan, J.; Zhao, H.; Zhou, Y. A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins, 2012, 80(8), 2080-2088.
[] [PMID: 22522696]
Pan, X.; Rijnbeek, P.; Yan, J.; Shen, H.B. Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks. BMC Genomics, 2018, 19(1), 511.
[] [PMID: 29970003]
The UniProt Consortium. UniProt: A worldwide hub of protein knowledge. Nucleic Acids Res., 2019, 47(D1), D506-D515.
[] [PMID: 30395287]
Ma, X.; Guo, J.; Sun, X. Sequence-based prediction of RNA-binding proteins using random forest with minimum redundancy maximum relevance feature selection. BioMed Res. Int., 2015.2015425810
[] [PMID: 26543860]
Altschul, S.F.; Madden, T.L.; Schäffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 1997, 25(17), 3389-3402.
[] [PMID: 9254694]
Fu, L.; Niu, B.; Zhu, Z.; Wu, S.; Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 2012, 28(23), 3150-3152.
[] [PMID: 23060610]
Wang, G.; Dunbrack, R.L. Jr PISCES: A protein sequence culling server. Bioinformatics, 2003, 19(12), 1589-1591.
[] [PMID: 12912846]
Cheng, C.W.; Su, E.C.; Hwang, J.K.; Sung, T.Y.; Hsu, W.L. Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics, 2008, 9(Suppl. 12), S6.
[] [PMID: 19091029]
Zhou, H.; Xue, B.; Zhou, Y. DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci., 2007, 16(5), 947-955.
[] [PMID: 17456745]
Zhao, H.; Yang, Y.; Zhou, Y. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res., 2011, 39(8), 3017-3025.
[] [PMID: 21183467]
El-Manzalawy, Y.; Abbas, M.; Malluhi, Q.; Honavar, V. FastRNABindR: Fast and accurate prediction of protein-RNA interface residues. PLoS One, 2016, 11(7)e0158445
[] [PMID: 27383535]
Tang, Y.; Liu, D.; Wang, Z.; Wen, T.; Deng, L. A boosting approach for prediction of protein-RNA binding residues. BMC Bioinformatics, 2017, 18(Suppl. 13), 465.
[] [PMID: 29219069]
Wang, L.; Brown, S.J. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 2006, 34(Web Server issue), W243-8,
[[http://10.1093/nar/gkl298]] [PMID: 16845003]
Wang, L.; Huang, C.; Yang, M.Q.; Yang, J.Y. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst. Biol., 2010, 4(Suppl. 1), S3.
[] [PMID: 20522253]
Ma, X.; Guo, J.; Wu, J.; Liu, H.; Yu, J.; Xie, J.; Sun, X. Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins, 2011, 79(4), 1230-1239.
[] [PMID: 21268114]
Allers, J.; Shamoo, Y. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol., 2001, 311(1), 75-86.
[] [PMID: 11469858]
Terribilini, M.; Sander, J.D.; Lee, J.H.; Zaback, P.; Jernigan, R.L.; Honavar, V.; Dobbs, D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res., 2007 35(Web Server issue), W578-84.,
[[10.1093/nar/gkm294]] [PMID: 17483510]
Clingman, C.C.; Deveau, L.M.; Hay, S.A.; Genga, R.M.; Shandilya, S.M.; Massi, F.; Ryder, S.P. Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite. eLife, 2014, 3, 3.
[] [PMID: 24935936]
Zhao, L.; Suarez, I.P.; Gauto, D.F.; Rasia, R.M.; Wang, J. The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A. Phys. Chem. Chem. Phys., 2018, 20(14), 9376-9388.
[] [PMID: 29565070]
Yang, X.X.; Deng, Z.L.; Liu, R. RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies. Proteins, 2014, 82(10), 2455-2471.
[] [PMID: 24854765]
McHugh, C.A.; Russell, P.; Guttman, M. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biol., 2014, 15(1), 203.
[] [PMID: 24467948]
Kloetgen, A.; Münch, P.C.; Borkhardt, A.; Hoell, J.I.; McHardy, A.C. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief. Funct. Genomics, 2015, 14(2), 102-114.
[] [PMID: 24951655]
Milek, M.; Wyler, E.; Landthaler, M. Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing. Semin. Cell Dev. Biol., 2012, 23(2), 206-212.
[] [PMID: 22212136]
Gagliardi, M.; Matarazzo, M.R. RIP: RNA Immunoprecipitation. Methods Mol. Biol., 2016, 1480, 73-86.
[] [PMID: 27659976]
Ule, J.; Jensen, K.; Mele, A.; Darnell, R.B. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods, 2005, 37(4), 376-386.
[] [PMID: 16314267]
Riley, K.J.; Steitz, J.A. The “Observer Effect” in genome-wide surveys of protein-RNA interactions. Mol. Cell, 2013, 49(4), 601-604.
[] [PMID: 23438856]
Brimacombe, R.; Stiege, W.; Kyriatsoulis, A.; Maly, P. Intra-RNA and RNA-protein cross-linking techniques in Escherichia coli ribosomes. Methods Enzymol., 1988, 164, 287-309.
[] [PMID: 3071669]
Keene, J.D.; Komisarow, J.M.; Friedersdorf, M.B. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protoc., 2006, 1(1), 302-307.
[] [PMID: 17406249]
Niranjanakumari, S.; Lasda, E.; Brazas, R.; Garcia-Blanco, M.A. Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. Methods, 2002, 26(2), 182-190.
[] [PMID: 12054895]
Peritz, T.; Zeng, F.; Kannanayakal, T.J.; Kilk, K.; Eiríksdóttir, E.; Langel, U.; Eberwine, J. Immunoprecipitation of mRNA-protein complexes. Nat. Protoc., 2006, 1(2), 577-580.
[] [PMID: 17406284]
Licatalosi, D.D.; Mele, A.; Fak, J.J.; Ule, J.; Kayikci, M.; Chi, S.W.; Clark, T.A.; Schweitzer, A.C.; Blume, J.E.; Wang, X.; Darnell, J.C.; Darnell, R.B. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature, 2008, 456(7221), 464-469.
[] [PMID: 18978773]
Hafner, M.; Landthaler, M.; Burger, L.; Khorshid, M.; Hausser, J.; Berninger, P.; Rothballer, A.; Ascano, M., Jr; Jungkamp, A.C.; Munschauer, M.; Ulrich, A.; Wardle, G.S.; Dewell, S.; Zavolan, M.; Tuschl, T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 2010, 141(1), 129-141.
[] [PMID: 20371350]
König, J.; Zarnack, K.; Rot, G.; Curk, T.; Kayikci, M.; Zupan, B.; Turner, D.J.; Luscombe, N.M.; Ule, J. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol., 2010, 17(7), 909-915.
[] [PMID: 20601959]
Conway, A.E.; Van Nostrand, E.L.; Pratt, G.A.; Aigner, S.; Wilbert, M.L.; Sundararaman, B.; Freese, P.; Lambert, N.J.; Sathe, S.; Liang, T.Y.; Essex, A.; Landais, S.; Burge, C.B.; Jones, D.L.; Yeo, G.W. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep., 2016, 15(3), 666-679.
[] [PMID: 27068461]
Van Nostrand, E.L.; Pratt, G.A.; Shishkin, A.A.; Gelboin-Burkhart, C.; Fang, M.Y.; Sundararaman, B.; Blue, S.M.; Nguyen, T.B.; Surka, C.; Elkins, K.; Stanton, R.; Rigo, F.; Guttman, M.; Yeo, G.W. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods, 2016, 13(6), 508-514.
[] [PMID: 27018577]
Khorshid, M.; Rodak, C.; Zavolan, M. CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res., 2011, 39(Database issue), D245-D252.
[] [PMID: 21087992]
Anders, G.; Mackowiak, S.D.; Jens, M.; Maaskola, J.; Kuntzagk, A.; Rajewsky, N.; Landthaler, M.; Dieterich, C. doRiNA: A database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res., 2012, 40(Database issue), D180-D186.
[] [PMID: 22086949]
Li, J.H.; Liu, S.; Zhou, H.; Qu, L.H.; Yang, J.H. starBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res., 2014, 42(Database issue), D92-D97.
[] [PMID: 24297251]
Dassi, E.; Re, A.; Leo, S.; Tebaldi, T.; Pasini, L.; Peroni, D.; Quattrone, A. AURA 2: Empowering discovery of post-transcriptional networks. Translation (Austin), 2014, 2(1)e27738
[[10.4161/trla.27738]] [PMID: 26779400]
Yang, Y.C.; Di, C.; Hu, B.; Zhou, M.; Liu, Y.; Song, N.; Li, Y.; Umetsu, J.; Lu, Z.J. CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics, 2015, 16, 51.
[] [PMID: 25652745]
Zhu, Y.; Xu, G.; Yang, Y.T.; Xu, Z.; Chen, X.; Shi, B.; Xie, D.; Lu, Z.J.; Wang, P. POSTAR2: Deciphering the post-transcriptional regulatory logics. Nucleic Acids Res., 2019, 47(D1), D203-D211.
[] [PMID: 30239819]
Corcoran, D.L.; Georgiev, S.; Mukherjee, N.; Gottwein, E.; Skalsky, R.L.; Keene, J.D.; Ohler, U. PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol., 2011, 12(8), R79.
[] [PMID: 21851591]
Uren, P.J.; Bahrami-Samani, E.; Burns, S.C.; Qiao, M.; Karginov, F.V.; Hodges, E.; Hannon, G.J.; Sanford, J.R.; Penalva, L.O.; Smith, A.D. Site identification in high-throughput RNA-protein interaction data. Bioinformatics, 2012, 28(23), 3013-3020.
[] [PMID: 23024010]
Blencowe, B.J.; Ahmad, S.; Lee, L.J. Current-generation high-throughput sequencing: Deepening insights into mammalian transcriptomes. Genes Dev., 2009, 23(12), 1379-1386.
[] [PMID: 19528315]
Derrien, T.; Estellé, J.; Marco Sola, S.; Knowles, D.G.; Raineri, E.; Guigó, R.; Ribeca, P. Fast computation and applications of genome mappability. PLoS One, 2012, 7(1)e30377
[] [PMID: 22276185]
Cheng, Z.; Zhou, S.; Guan, J. Computationally predicting protein-RNA interactions using only positive and unlabeled examples. J. Bioinform. Comput. Biol., 2015, 13(3)1541005
[] [PMID: 25790785]
Varma, S.; Simon, R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics, 2006, 7, 91.
[] [PMID: 16504092]
Xue, B.; Dunbrack, R.L.; Williams, R.W.; Dunker, A.K.; Uversky, V.N. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim. Biophys. Acta, 2010, 1804(4), 996-1010.
[] [PMID: 20100603]
Conicella, A.E.; Zerze, G.H.; Mittal, J.; Fawzi, N.L. ALS mutations disrupt phase separation mediated by α-helical structure in the TDP-43 Low-complexity C-terminal domain. Structure, 2016, 24(9), 1537-1549.
[] [PMID: 27545621]
Ryan, VH.; Dignon, GL.; Zerze, GH.; Chabata, CV. Silva, R Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation. Mol. Cell, 2018, 69, 465-479.
Vernon, R.M.; Chong, P.A.; Tsang, B.; Kim, T.H.; Bah, A.; Farber, P.; Lin, H.; Forman-Kay, J.D. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. eLife, 2018, 7, 7.
[] [PMID: 29424691]
Ferrolino, M.C.; Mitrea, D.M.; Michael, J.R.; Kriwacki, R.W. Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms. Nat. Commun., 2018, 9(1), 5064.
[] [PMID: 30498217]
Zhou, H.X.; Nguemaha, V.; Mazarakos, K.; Qin, S. Why Do Disordered and Structured Proteins Behave Differently in Phase Separation? Trends Biochem. Sci., 2018, 43(7), 499-516.
[] [PMID: 29716768]
Iborra, F.J. Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation? Theor. Biol. Med. Model., 2007, 4, 15.
[] [PMID: 17430588]
Dignon, G.L.; Zheng, W.; Kim, Y.C.; Best, R.B.; Mittal, J. Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Comput. Biol., 2018, 14(1)e1005941
[] [PMID: 29364893]
Larrañaga, P.; Calvo, B.; Santana, R.; Bielza, C.; Galdiano, J.; Inza, I.; Lozano, J.A.; Armañanzas, R.; Santafé, G.; Pérez, A.; Robles, V. Machine learning in bioinformatics. Brief. Bioinform., 2006, 7(1), 86-112.
[] [PMID: 16761367]
Bhaskar, H.; Hoyle, D.C.; Singh, S. Machine learning in bioinformatics: a brief survey and recommendations for practitioners. Comput. Biol. Med., 2006, 36(10), 1104-1125.
[] [PMID: 16226240]
Narayanan, A.; Keedwell, E.C.; Olsson, B. Artificial intelligence techniques for bioinformatics. Appl. Bioinformatics, 2002, 1(4), 191-222.
[PMID: 15130837]
Tarca, A.L.; Carey, V.J.; Chen, X.W.; Romero, R.; Drăghici, S. Machine learning and its applications to biology. PLOS Comput. Biol., 2007, 3(6)e116
[] [PMID: 17604446]
Han, L.Y.; Cai, C.Z.; Lo, S.L.; Chung, M.C.; Chen, Y.Z. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA, 2004, 10(3), 355-368.
[] [PMID: 14970381]
Muppirala, U.K.; Honavar, V.G.; Dobbs, D. Predicting RNA-protein interactions using only sequence information. BMC Bioinformatics, 2011, 12, 489.
[] [PMID: 22192482]
Kumar, M.; Gromiha, M.M.; Raghava, G.P. SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. J. Mol. Recognit., 2011, 24(2), 303-313.
[] [PMID: 20677174]
Suresh, V.; Liu, L.; Adjeroh, D.; Zhou, X. RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information. Nucleic Acids Res., 2015, 43(3), 1370-1379.
[] [PMID: 25609700]
Shen, W.J.; Cui, W.; Chen, D.; Zhang, J.; Xu, J. RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence. Molecules, 2018, 23(3), 23.
[] [PMID: 29495575]
Zhang, X.; Liu, S. RBPPred: predicting RNA-binding proteins from sequence using SVM. Bioinformatics, 2017, 33(6), 854-862.
[PMID: 27993780]
Agostini, F.; Zanzoni, A.; Klus, P.; Marchese, D.; Cirillo, D.; Tartaglia, G.G. catRAPID omics: A web server for large-scale prediction of protein-RNA interactions. Bioinformatics, 2013, 29(22), 2928-2930.
[] [PMID: 23975767]
Lu, Q.; Ren, S.; Lu, M.; Zhang, Y.; Zhu, D.; Zhang, X.; Li, T. Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics, 2013, 14, 651.
[] [PMID: 24063787]
Pancaldi, V.; Bähler, J. In silico characterization and prediction of global protein-mRNA interactions in yeast. Nucleic Acids Res., 2011, 39(14), 5826-5836.
[] [PMID: 21459850]
Livi, C.M.; Blanzieri, E. Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. BMC Bioinformatics, 2014, 15, 123.
[] [PMID: 24780077]
Armaos, A.; Cirillo, D.; Gaetano Tartaglia, G. omiXcore: A web server for prediction of protein interactions with large RNA. Bioinformatics, 2017, 33(19), 3104-3106.
[] [PMID: 28637296]
Jeong, E.; Chung, I.F.; Miyano, S. A neural network method for identification of RNA-interacting residues in protein. Genome Inform, 2004, 15(1), 105-116.
[PMID: 15712114]
Kumar, M.; Gromiha, M.M.; Raghava, G.P. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, 2008, 71(1), 189-194.
[] [PMID: 17932917]
Liu, Z.P.; Wu, L.Y.; Wang, Y.; Zhang, X.S.; Chen, L. Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, 2010, 26(13), 1616-1622.
[] [PMID: 20483814]
Ma, X.; Guo, J.; Xiao, K.; Sun, X. PRBP: Prediction of RNA-binding proteins using a random forest algorithm combined with an RNA-binding residue predictor. IEEE/. ACM Trans Comput. Biol. Bioinform, 2015, 12, 1385-1393.
[[] [PMID: 26671809]
Sun, M.; Wang, X.; Zou, C.; He, Z.; Liu, W.; Li, H. Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors. BMC Bioinformatics, 2016, 17(1), 231.
[] [PMID: 27266516]
Carson, M.B.; Langlois, R.; Lu, H. NAPS: A residue-level nucleic acid-binding prediction server. Nucleic Acids Res., 2010, 38(Web Server issue)W431-5,
[[10.1093/nar/gkq361]] [PMID: 20478832]
Pai, P.P.; Dash, T.; Mondal, S. Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach. J. Theor. Biol., 2017, 418, 77-83.
[] [PMID: 28137600]
Kim, O.T.; Yura, K.; Go, N. Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res., 2006, 34(22), 6450-6460.
[] [PMID: 17130160]
Kazan, H.; Ray, D.; Chan, E.T.; Hughes, T.R.; Morris, Q. RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLOS Comput. Biol., 2010, 6e1000832
[] [PMID: 20617199]
Maticzka, D.; Lange, S.J.; Costa, F.; Backofen, R. GraphProt: Modeling binding preferences of RNA-binding proteins. Genome Biol., 2014, 15(1), R17.
[] [PMID: 24451197]
Orenstein, Y.; Wang, Y.; Berger, B. RCK: Accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinformatics, 2016, 32(12), i351-i359.
[] [PMID: 27307637]
Heller, D.; Krestel, R.; Ohler, U.; Vingron, M.; Marsico, A. ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. Nucleic Acids Res., 2017, 45(19), 11004-11018.
[] [PMID: 28977546]
Tuvshinjargal, N.; Lee, W.; Park, B.; Han, K. PRIdictor: Protein-RNA interaction predictor. Biosystems, 2016, 139, 17-22.
[] [PMID: 26607710]
Choi, D.; Park, B.; Chae, H.; Lee, W.; Han, K. Predicting protein-binding regions in RNA using nucleotide profiles and compositions. BMC Syst. Biol., 2017, 11(Suppl. 2), 16.
[] [PMID: 28361677]
Mann, M.; Wright, P.R.; Backofen, R. IntaRNA 2.0: Enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res., 2017, 45(W1), W435-W439.
[] [PMID: 28472523]
Gawronski, A.R.; Uhl, M.; Zhang, Y.; Lin, Y.Y.; Niknafs, Y.S.; Ramnarine, V.R.; Malik, R.; Feng, F.; Chinnaiyan, A.M.; Collins, C.C.; Sahinalp, S.C.; Backofen, R. MechRNA: Prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinformatics, 2018, 34(18), 3101-3110.
[] [PMID: 29617966]
Fernandez, M.; Kumagai, Y.; Standley, D.M.; Sarai, A.; Mizuguchi, K.; Ahmad, S. Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics, 2011, 12(Suppl. 13), S5.
[] [PMID: 22373260]
Luo, J.; Liu, L.; Venkateswaran, S.; Song, Q.; Zhou, X. RPI-Bind: A structure-based method for accurate identification of RNA-protein binding sites. Sci. Rep., 2017, 7(1), 614.
[] [PMID: 28377624]
Alipanahi, B.; Delong, A.; Weirauch, M.T.; Frey, B.J. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat. Biotechnol., 2015, 33(8), 831-838.
[] [PMID: 26213851]
Pan, X.; Fan, Y.X.; Yan, J.; Shen, H.B. IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. BMC Genomics, 2016, 17, 582.
[] [PMID: 27506469]
Pan, X.; Shen, H.B. RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. BMC Bioinformatics, 2017, 18(1), 136.
[] [PMID: 28245811]
Pan, X.; Shen, H.B. Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinformatics, 2018, 34(20), 3427-3436.
[] [PMID: 29722865]
Budach, S.; Marsico, A. pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks. Bioinformatics, 2018, 34(17), 3035-3037.
[] [PMID: 29659719]
Zhang, S.; Zhou, J.; Hu, H.; Gong, H.; Chen, L.; Cheng, C.; Zeng, J. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res., 2016, 44(4)e32
[] [PMID: 26467480]
Peng, C.R.; Liu, L.; Niu, B.; Lv, Y.L.; Li, M.J.; Yuan, Y.L.; Zhu, Y.B.; Lu, W.C.; Cai, Y.D. Prediction of RNA-binding proteins by voting systems. J. Biomed. Biotechnol., 2011, 2011506205
[] [PMID: 21826121]
Walia, R.R.; Xue, L.C.; Wilkins, K.; El-Manzalawy, Y.; Dobbs, D.; Honavar, V. RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins. PLoS One, 2014, 9(5)e97725
[] [PMID: 24846307]
Yang, X.; Wang, J.; Sun, J.; Liu, R. SNBRFinder: A sequence-based hybrid algorithm for enhanced prediction of nucleic acid-binding residues. PLoS One, 2015, 10(7)e0133260
[] [PMID: 26176857]
Ren, H.; Shen, Y. RNA-binding residues prediction using structural features. BMC Bioinformatics, 2015, 16, 249.
[] [PMID: 26254826]
Chen, Y.C.; Lim, C. Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 2008, 36(5)e29
[] [PMID: 18276647]
Zhao, B.; Xue, B. Decision-tree based meta-strategy improved accuracy of disorder prediction and identified novel disordered residues inside binding motifs. Int. J. Mol. Sci., 2018, 19(10), 19.
[] [PMID: 30301243]
Zhao, B.; Xue, B. Significant improvement of miRNA target prediction accuracy in large datasets using meta-strategy based on comprehensive voting and artificial neural networks. BMC Genomics, 2019, 20(1), 158.
[] [PMID: 30813885]
Garnier, J.; Osguthorpe, D.J.; Robson, B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol., 1978, 120(1), 97-120.
[] [PMID: 642007]
Rost, B.; Fariselli, P.; Casadio, R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 1996, 5(8), 1704-1718.
[] [PMID: 8844859]
Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 1999, 292(2), 195-202.
[] [PMID: 10493868]
Tong, J.; Jiang, P.; Lu, Z.H. RISP: A web-based server for prediction of RNA-binding sites in proteins. Comput. Methods Programs Biomed., 2008, 90(2), 148-153.
[] [PMID: 18261823]
Wang, C.C.; Fang, Y.; Xiao, J.; Li, M. Identification of RNA-binding sites in proteins by integrating various sequence information. Amino Acids, 2011, 40(1), 239-248.
[] [PMID: 20549269]
Choi, S.; Han, K. Prediction of RNA-binding amino acids from protein and RNA sequences. BMC Bioinformatics, 2011, 12(Suppl. 13), S7.
[] [PMID: 22373313]
Spriggs, R.V.; Murakami, Y.; Nakamura, H.; Jones, S. Protein function annotation from sequence: Prediction of residues interacting with RNA. Bioinformatics, 2009, 25(12), 1492-1497.
[] [PMID: 19389733]
Towfic, F.; Caragea, C.; Gemperline, D.C.; Dobbs, D.; Honavar, V. Struct-NB: Predicting protein-RNA binding sites using structural features. Int. J. Data Min. Bioinform., 2010, 4(1), 21-43.
[] [PMID: 20300450]
Choi, S.; Han, K. Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. Comput. Biol. Med., 2013, 43(11), 1687-1697.
[] [PMID: 24209914]
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 1983, 22(12), 2577-2637.
[] [PMID: 6667333]
Hubbard, S.J.; Thornton, J.M. ‘NACCESS’, computer program; Department of Biochemistry and Molecular Biology, University College: London, 1993.
Heffernan, R.; Paliwal, K.; Lyons, J.; Dehzangi, A.; Sharma, A.; Wang, J.; Sattar, A.; Yang, Y.; Zhou, Y. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Sci. Rep., 2015, 5, 11476.
[] [PMID: 26098304]
McGuffin, L.J.; Bryson, K.; Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics, 2000, 16(4), 404-405.
[] [PMID: 10869041]
Frishman, D.; Argos, P. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng., 1996, 9(2), 133-142.
[] [PMID: 9005434]
Faraggi, E.; Zhang, T.; Yang, Y.; Kurgan, L.; Zhou, Y. SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J. Comput. Chem., 2012, 33(3), 259-267.
[] [PMID: 22045506]
Petersen, B.; Petersen, T.N.; Andersen, P.; Nielsen, M.; Lundegaard, C. A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct. Biol., 2009, 9, 51.
[] [PMID: 19646261]
Drozdetskiy, A.; Cole, C.; Procter, J.; Barton, G.J. JPred4: A protein secondary structure prediction server. Nucleic Acids Res., 2015, 43(W1)W389-94
[] [PMID: 25883141]
Steffen, P.; Voss, B.; Rehmsmeier, M.; Reeder, J.; Giegerich, R. RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics, 2006, 22(4), 500-503.
[] [PMID: 16357029]
Kyte, J.; Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982, 157(1), 105-132.
[] [PMID: 7108955]
Lehninger, A.; Nelson, D.; Cox, M. Principles of Biochemistry; Worth: New York, 1993.
Kaur, H.; Raghava, G.P. Prediction of beta-turns in proteins from multiple alignment using neural network. Protein Sci., 2003, 12(3), 627-634.
[] [PMID: 12592033]
Kaur, H.; Raghava, G.P. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci., 2003, 12(5), 923-929.
[] [PMID: 12717015]
Kumar, M.; Bhasin, M.; Natt, N.K.; Raghava, G.P. BhairPred: prediction of beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques.. Nucleic Acids Res., 2005, 33(Web Server issue)W154-9,
[[10.1093/nar/gki588]] [PMID: 15988830]
Maetschke, S.R.; Yuan, Z. Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics, 2009, 10, 341.
[] [PMID: 19835626]
Kumar, M.; Gromiha, M.M.; Raghava, G.P. Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics, 2007, 8, 463.
[] [PMID: 18042272]
Henikoff, S.; Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 1992, 89(22), 10915-10919.
[] [PMID: 1438297]
Wang, Y.; Xue, Z.; Shen, G.; Xu, J. PRINTR: prediction of RNA binding sites in proteins using SVM and profiles. Amino Acids, 2008, 35(2), 295-302.
[] [PMID: 18235992]
Li, Q.; Cao, Z.; Liu, H. Improve the prediction of RNA-binding residues using structural neighbours. Protein Pept. Lett., 2010, 17(3), 287-296.
[] [PMID: 19508202]
Huang, Y.F.; Chiu, L.Y.; Huang, C.C.; Huang, C.K. Predicting RNA-binding residues from evolutionary information and sequence conservation. BMC Genomics, 2010, 11(Suppl. 4), S2.
[] [PMID: 21143803]
Veljkovic, V.; Veljkovic, N.; Esté, J.A.; Hüther, A.; Dietrich, U. Application of the EIIP/ISM bioinformatics concept in development of new drugs. Curr. Med. Chem., 2007, 14(4), 441-453.
[] [PMID: 17305545]
Miao, Z.; Westhof, E. Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score. Nucleic Acids Res., 2015, 43(11), 5340-5351.
[] [PMID: 25940624]
Xue, B.; Lipps, D.; Devineni, S. Integrated strategy improves the prediction accuracy of miRNA in large dataset. PLoS One, 2016, 11(12)e0168392
[] [PMID: 28002428]
Wen, J.; Wang, J.; Zhang, Q.; Guo, D. A heuristic model for computational prediction of human branch point sequence. BMC Bioinformatics, 2017, 18(1), 459.
[] [PMID: 29065858]
Zhou, Y.; Zeng, P.; Li, Y.H.; Zhang, Z.; Cui, Q. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Res., 2016, 44(10)e91
[] [PMID: 26896799]
Antunes, D.; Jorge, N.A.N.; Caffarena, E.R.; Passetti, F. Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools. Front. Genet., 2018, 8, 231.
[] [PMID: 29403526]
Huang, L.; Lilley, D.M.J. The Kink Turn, a Key Architectural Element in RNA Structure. J. Mol. Biol., 2016, 428(5 Pt A), 790-801.
[] [PMID: 26522935]

© 2022 Bentham Science Publishers | Privacy Policy