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Journal articles on the topic 'RNA-binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

Muckstein, U., H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker. "Thermodynamics of RNA-RNA binding." Bioinformatics 22, no. 10 (January 29, 2006): 1177–82. http://dx.doi.org/10.1093/bioinformatics/btl024.

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2

Hallegger, M., A. Taschner, and M. F. Jantsch. "RNA aptamers binding the double-stranded RNA-binding domain." RNA 12, no. 11 (September 27, 2006): 1993–2004. http://dx.doi.org/10.1261/rna.125506.

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3

Muto, Yutaka, Chris Oubridge, and Kiyoshi Nagai. "RNA-binding proteins: TRAPping RNA bases." Current Biology 10, no. 1 (January 2000): R19—R21. http://dx.doi.org/10.1016/s0960-9822(99)00250-x.

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4

Kotelnikov, R. N., S. G. Shpiz, A. I. Kalmykova, and V. A. Gvozdev. "RNA-binding proteins in RNA interference." Molecular Biology 40, no. 4 (July 2006): 528–40. http://dx.doi.org/10.1134/s0026893306040054.

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5

Serin, Guillaume, Gérard Joseph, Laurence Ghisolfi, Marielle Bauzan, Monique Erard, François Amalric, and Philippe Bouvet. "Two RNA-binding Domains Determine the RNA-binding Specificity of Nucleolin." Journal of Biological Chemistry 272, no. 20 (May 16, 1997): 13109–16. http://dx.doi.org/10.1074/jbc.272.20.13109.

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6

Sastry, Srin, and Barbara M. Ross. "RNA-binding site in T7 RNA polymerase." Proceedings of the National Academy of Sciences 95, no. 16 (August 4, 1998): 9111–16. http://dx.doi.org/10.1073/pnas.95.16.9111.

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Recent models of RNA polymerase transcription complexes have invoked the idea that enzyme-nascent RNA contacts contribute to the stability of the complexes. Although much progress on this topic has been made with the multisubunit Escherichia coli RNA polymerase, there is a paucity of information regarding the structure of single-subunit phage RNA polymerase transcription complexes. Here, we photo-cross-linked the RNA in a T7 RNA polymerase transcription complex and mapped a major contact site between amino acid residues 144 and 168 and probably a minor contact between residues 1 and 93. These regions of the polymerase are proposed to interact with the emerging RNA during transcription because the 5′ end of the RNA was cross-linked. The contacts are both ionic and nonionic (hydrophobic). The specific inhibitor of T7 transcription, T7 lysozyme, does not compete with T7 RNA polymerase for RNA cross-linking, implying that the RNA does not bind the lysozyme. However, lysozyme may act indirectly via a conformational change in the polymerase. In the current model, the DNA template lies in the polymerase cleft and the fingers subdomain may contact or maintain a template bubble, and a region in the N terminus forms a partly solvent-accessible binding channel for the emerging RNA.

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7

Singh, Arunima. "RNA-binding protein kinetics." Nature Methods 18, no. 4 (April 2021): 335. http://dx.doi.org/10.1038/s41592-021-01122-6.

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8

SUGITA, Mamoru, and Masahiro SUGIURA. "Chloroplast RNA-binding Proteins." Nippon Nōgeikagaku Kaishi 71, no. 11 (1997): 1177–79. http://dx.doi.org/10.1271/nogeikagaku1924.71.1177.

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9

Larochelle, Stéphane. "RNA-binding proteome redux." Nature Methods 16, no. 3 (February 27, 2019): 219. http://dx.doi.org/10.1038/s41592-019-0349-3.

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10

Laird-Offringa, Ite A., and Joel G. Belasco. "RNA-binding proteins tamed." Nature Structural & Molecular Biology 5, no. 8 (August 1998): 665–68. http://dx.doi.org/10.1038/1356.

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11

Goers, Emily S., Rodger B. Voelker, Devika P. Gates, and J. Andrew Berglund. "RNA Binding Specificity ofDrosophilaMuscleblind†." Biochemistry 47, no. 27 (July 2008): 7284–94. http://dx.doi.org/10.1021/bi702252d.

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12

Smith, Colin A., Valerie Calabro, and Alan D. Frankel. "An RNA-Binding Chameleon." Molecular Cell 6, no. 5 (November 2000): 1067–76. http://dx.doi.org/10.1016/s1097-2765(00)00105-2.

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13

Goodall, Greg, Jonathan Levy, Maria Mieszczak, and Witold Filipowicz. "Plant RNA-binding proteins." Molecular Biology Reports 14, no. 2-3 (1990): 137. http://dx.doi.org/10.1007/bf00360447.

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14

Nickelsen, J�rg. "Chloroplast RNA-binding proteins." Current Genetics 43, no. 6 (September 1, 2003): 392–99. http://dx.doi.org/10.1007/s00294-003-0425-0.

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15

Shimada, Naohiko, Reiko Iwase, Tetsuji Yamaoka, and Akira Murakami. "Design of RNA-Binding Oligopeptides Based on Information of RNA-Binding Protein." Polymer Journal 35, no. 6 (June 2003): 507–12. http://dx.doi.org/10.1295/polymj.35.507.

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16

Stefl, Richard, Ming Xu, Lenka Skrisovska, Ronald B. Emeson, and Frédéric H. T. Allain. "Structure and Specific RNA Binding of ADAR2 Double-Stranded RNA Binding Motifs." Structure 14, no. 2 (February 2006): 345–55. http://dx.doi.org/10.1016/j.str.2005.11.013.

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17

Windbichler, Nikolai, and Renée Schroeder. "Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer." Nature Protocols 1, no. 2 (June 27, 2006): 637–40. http://dx.doi.org/10.1038/nprot.2006.95.

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18

Gonzalez-Rivera, Juan C., Asuka A. Orr, Sean M. Engels, Joseph M. Jakubowski, Mark W. Sherman, Katherine N. O'Connor, Tomas Matteson, Brendan C. Woodcock, Lydia M. Contreras, and Phanourios Tamamis. "Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding." Computational and Structural Biotechnology Journal 18 (2020): 137–52. http://dx.doi.org/10.1016/j.csbj.2019.12.003.

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19

Tuccinardi, Tiziano. "Binding-interaction prediction of RNA-binding ligands." Future Medicinal Chemistry 3, no. 6 (April 2011): 723–33. http://dx.doi.org/10.4155/fmc.11.25.

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20

Zhu, J., K. Gopinath, A. Murali, G. Yi, S. D. Hayward, H. Zhu, and C. Kao. "RNA-binding proteins that inhibit RNA virus infection." Proceedings of the National Academy of Sciences 104, no. 9 (February 20, 2007): 3129–34. http://dx.doi.org/10.1073/pnas.0611617104.

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21

Fu, Yuan, and Anne Baranger. "MBNL1-RNA Interactions: Binding-Induced Rna Conformational Changes." Biophysical Journal 102, no. 3 (January 2012): 75a. http://dx.doi.org/10.1016/j.bpj.2011.11.438.

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22

Jolma, Arttu, Jilin Zhang, Estefania Mondragón, Ekaterina Morgunova, Teemu Kivioja, Kaitlin U. Laverty, Yimeng Yin, et al. "Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences." Genome Research 30, no. 7 (July 2020): 962–73. http://dx.doi.org/10.1101/gr.258848.119.

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23

Brooks, Roman, Christian R. Eckmann, and Michael F. Jantsch. "The double-stranded RNA-binding domains ofXenopus laevisADAR1 exhibit different RNA-binding behaviors." FEBS Letters 434, no. 1-2 (August 28, 1998): 121–26. http://dx.doi.org/10.1016/s0014-5793(98)00963-6.

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24

Burd, C. G., E. L. Matunis, and G. Dreyfuss. "The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities." Molecular and Cellular Biology 11, no. 7 (July 1991): 3419–24. http://dx.doi.org/10.1128/mcb.11.7.3419-3424.1991.

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The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or efficiently. Contiguous two-domain combinations were required for efficient RNA binding, and each pairwise combination (I/II, II/III, and III/IV) had a distinct RNA-binding activity. Specific poly(A)-binding activity was found only in the two amino-terminal RBDs (I/II) which, interestingly, are dispensable for viability of yeast cells, whereas the activity that is sufficient to rescue lethality of a PABP-deleted strain is in the carboxyl-terminal RBDs (III/IV). We conclude that the PABP is a multifunctional RNA-binding protein that has at least two distinct and separable activities: RBDs I/II, which most likely function in binding the PABP to mRNA through the poly(A) tail, and RBDs III/IV, which may function through binding either to a different part of the same mRNA molecule or to other RNA(s).

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25

Burd, C. G., E. L. Matunis, and G. Dreyfuss. "The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities." Molecular and Cellular Biology 11, no. 7 (July 1991): 3419–24. http://dx.doi.org/10.1128/mcb.11.7.3419.

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The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or efficiently. Contiguous two-domain combinations were required for efficient RNA binding, and each pairwise combination (I/II, II/III, and III/IV) had a distinct RNA-binding activity. Specific poly(A)-binding activity was found only in the two amino-terminal RBDs (I/II) which, interestingly, are dispensable for viability of yeast cells, whereas the activity that is sufficient to rescue lethality of a PABP-deleted strain is in the carboxyl-terminal RBDs (III/IV). We conclude that the PABP is a multifunctional RNA-binding protein that has at least two distinct and separable activities: RBDs I/II, which most likely function in binding the PABP to mRNA through the poly(A) tail, and RBDs III/IV, which may function through binding either to a different part of the same mRNA molecule or to other RNA(s).

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26

Maticzka, Daniel, Sita J. Lange, Fabrizio Costa, and Rolf Backofen. "GraphProt: modeling binding preferences of RNA-binding proteins." Genome Biology 15, no. 1 (2014): R17. http://dx.doi.org/10.1186/gb-2014-15-1-r17.

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27

Yu, Hui, Jing Wang, Quanhu Sheng, Qi Liu, and Yu Shyr. "beRBP: binding estimation for human RNA-binding proteins." Nucleic Acids Research 47, no. 5 (December 27, 2018): e26-e26. http://dx.doi.org/10.1093/nar/gky1294.

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Abstract Identifying binding targets of RNA-binding proteins (RBPs) can greatly facilitate our understanding of their functional mechanisms. Most computational methods employ machine learning to train classifiers on either RBP-specific targets or pooled RBP–RNA interactions. The former strategy is more powerful, but it only applies to a few RBPs with a large number of known targets; conversely, the latter strategy sacrifices prediction accuracy for a wider application, since specific interaction features are inevitably obscured through pooling heterogeneous datasets. Here, we present beRBP, a dual approach to predict human RBP–RNA interaction given PWM of a RBP and one RNA sequence. Based on Random Forests, beRBP not only builds a specific model for each RBP with a decent number of known targets, but also develops a general model for RBPs with limited or null known targets. The specific and general models both compared well with existing methods on three benchmark datasets. Notably, the general model achieved a better performance than existing methods on most novel RBPs. Overall, as a composite solution overarching the RBP-specific and RBP-General strategies, beRBP is a promising tool for human RBP binding estimation with good prediction accuracy and a broad application scope.

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28

Ciafrè, Silvia Anna, and Silvia Galardi. "microRNAs and RNA-binding proteins." RNA Biology 10, no. 6 (June 2013): 934–42. http://dx.doi.org/10.4161/rna.24641.

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29

DeLisle, A. J. "RNA-Binding Protein from Arabidopsis." Plant Physiology 102, no. 1 (May 1, 1993): 313–14. http://dx.doi.org/10.1104/pp.102.1.313.

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30

Tang, Lei. "Examining global RNA-binding proteomes." Nature Methods 16, no. 2 (January 30, 2019): 144. http://dx.doi.org/10.1038/s41592-019-0321-2.

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31

Strack, Rita. "Predicting RNA–protein binding affinity." Nature Methods 16, no. 6 (May 30, 2019): 460. http://dx.doi.org/10.1038/s41592-019-0445-4.

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32

Berens, Christian, Alison Thain, and Renée Schroeder. "A tetracycline-binding RNA aptamer." Bioorganic & Medicinal Chemistry 9, no. 10 (October 2001): 2549–56. http://dx.doi.org/10.1016/s0968-0896(01)00063-3.

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33

Zamore, Phillip D., Maria L. Zapp, and Michael R. Green. "RNA binding: βS and basics." Nature 348, no. 6301 (December 1990): 485–86. http://dx.doi.org/10.1038/348485a0.

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34

Antson, Alfred A. "Single stranded RNA binding proteins." Current Opinion in Structural Biology 10, no. 1 (February 2000): 87–94. http://dx.doi.org/10.1016/s0959-440x(99)00054-8.

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35

Nafisi, Sh, A. Shadaloi, A. Feizbakhsh, and H. A. Tajmir-Riahi. "RNA binding to antioxidant flavonoids." Journal of Photochemistry and Photobiology B: Biology 94, no. 1 (January 2009): 1–7. http://dx.doi.org/10.1016/j.jphotobiol.2008.08.001.

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36

Luo, Zheng, Qin Yang, and Li Yang. "RNA Structure Switches RBP Binding." Molecular Cell 64, no. 2 (October 2016): 219–20. http://dx.doi.org/10.1016/j.molcel.2016.10.006.

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37

Purnell, B. A. "Noncoding RNA helps protein binding." Science 350, no. 6263 (November 19, 2015): 923–25. http://dx.doi.org/10.1126/science.350.6263.923-o.

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38

Holmqvist, Erik, and Jörg Vogel. "RNA-binding proteins in bacteria." Nature Reviews Microbiology 16, no. 10 (July 11, 2018): 601–15. http://dx.doi.org/10.1038/s41579-018-0049-5.

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39

ARNEZ, JOHN G., and JEAN CAVARELLI. "Structures of RNA-binding proteins." Quarterly Reviews of Biophysics 30, no. 3 (August 1997): 195–240. http://dx.doi.org/10.1017/s0033583597003351.

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40

Toth, Miklos. "RNA binding proteins in epilepsy." Gene Function & Disease 2, no. 2-3 (October 2001): 95–98. http://dx.doi.org/10.1002/1438-826x(200110)2:2/3<95::aid-gnfd95>3.0.co;2-i.

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41

De Conti, Laura, Marco Baralle, and Emanuele Buratti. "Neurodegeneration and RNA-binding proteins." Wiley Interdisciplinary Reviews: RNA 8, no. 2 (September 22, 2016): e1394. http://dx.doi.org/10.1002/wrna.1394.

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42

Copeland, Paul R., and Donna M. Driscoll. "RNA binding proteins and selenocysteine." BioFactors 14, no. 1-4 (2001): 11–16. http://dx.doi.org/10.1002/biof.5520140103.

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43

Choi, Kwang-Ho, Seong-Ryul Kim, Sung-Wan Kim, Tae-Won Goo, Seok-Woo Kang, and Seoung-Won Park. "Characterization of the RNA binding protein-1 gene promoter of the silkworm silk grands." Journal of Sericultural and Entomological Science 52, no. 1 (April 30, 2014): 39–44. http://dx.doi.org/10.7852/jses.2014.52.1.39.

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44

Rouda, Susan, and Emmanuel Skordalakes. "Structure of the RNA-Binding Domain of Telomerase: Implications for RNA Recognition and Binding." Structure 15, no. 11 (November 2007): 1403–12. http://dx.doi.org/10.1016/j.str.2007.09.007.

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45

Ginisty, Hervé, François Amalric, and Philippe Bouvet. "Two Different Combinations of RNA-binding Domains Determine the RNA Binding Specificity of Nucleolin." Journal of Biological Chemistry 276, no. 17 (January 18, 2001): 14338–43. http://dx.doi.org/10.1074/jbc.m011120200.

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46

Tran, Kiet, Michelle Arkin, and Peter Beal. "Tethering in RNA: An RNA-Binding Fragment Discovery Tool." Molecules 20, no. 3 (March 4, 2015): 4148–61. http://dx.doi.org/10.3390/molecules20034148.

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47

Li, Xinyi, Wenchen Pu, Song Chen, and Yong Peng. "Therapeutic targeting of RNA-binding protein by RNA-PROTAC." Molecular Therapy 29, no. 6 (June 2021): 1940–42. http://dx.doi.org/10.1016/j.ymthe.2021.04.032.

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48

Fung, P. A., R. Labrecque, and T. Pederson. "RNA-dependent phosphorylation of a nuclear RNA binding protein." Proceedings of the National Academy of Sciences 94, no. 4 (February 18, 1997): 1064–68. http://dx.doi.org/10.1073/pnas.94.4.1064.

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49

Sohrabi-Jahromi, Salma, and Johannes Söding. "Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins." Bioinformatics 37, Supplement_1 (July 1, 2021): i308—i316. http://dx.doi.org/10.1093/bioinformatics/btab300.

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Abstract Motivation Understanding how proteins recognize their RNA targets is essential to elucidate regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or have multiple domains that allow them to bind to RNA in a multivalent, cooperative manner. They can thereby achieve higher specificity and affinity than proteins with a single RNA-binding domain. However, current approaches to de novo discovery of RNA binding motifs do not take multivalent binding into account. Results We present Bipartite Motif Finder (BMF), which is based on a thermodynamic model of RBPs with two cooperatively binding RNA-binding domains. We show that bivalent binding is a common strategy among RBPs, yielding higher affinity and sequence specificity. We furthermore illustrate that the spatial geometry between the binding sites can be learned from bound RNA sequences. These discovered bipartite motifs are consistent with previously known motifs and binding behaviors. Our results demonstrate the importance of multivalent binding for RNA-binding proteins and highlight the value of bipartite motif models in representing the multivalency of protein-RNA interactions. Availability and implementation BMF source code is available at https://github.com/soedinglab/bipartite_motif_finder under a GPL license. The BMF web server is accessible at https://bmf.soedinglab.org. Supplementary information Supplementary data are available at Bioinformatics online.

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50

Si, Jingna, Jing Cui, Jin Cheng, and Rongling Wu. "Computational Prediction of RNA-Binding Proteins and Binding Sites." International Journal of Molecular Sciences 16, no. 11 (November 3, 2015): 26303–17. http://dx.doi.org/10.3390/ijms161125952.

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