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Volumn 42, Issue 3, 2014, Pages

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ASPARAGINE; CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3; PHENYLALANINE; RNA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

EID: 84896701134     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1299     Document Type: Article
Times cited : (28)

References (49)
  • 1
    • 0037448593 scopus 로고    scopus 로고
    • Functional genomics: RNA sets the standard
    • Tuschl, T. (2003) Functional genomics: RNA sets the standard. Nature, 421, 268-272.
    • (2003) Nature , vol.421 , pp. 268-272
    • Tuschl, T.1
  • 2
    • 60149093432 scopus 로고    scopus 로고
    • RNA and disease
    • Cooper, T.A., Wan, L. and Dreyfuss, G. (2009) RNA and disease. Cell, 136, 777-793.
    • (2009) Cell , vol.136 , pp. 777-793
    • Cooper, T.A.1    Wan, L.2    Dreyfuss, G.3
  • 5
    • 0032919203 scopus 로고    scopus 로고
    • The RNAbinding properties of SMN: Deletion analysis of the zebrafish orthologue defines domains conserved in evolution
    • Bertrandy, S., Burlet, P., Clermont, O., Huber, C., Fondrat, C., Thierry-Mieg, D., Munnich, A. and Lefebvre, S. (1999) The RNAbinding properties of SMN: deletion analysis of the zebrafish orthologue defines domains conserved in evolution. Hum. Mol. Genet., 8, 775-782.
    • (1999) Hum. Mol. Genet , vol.8 , pp. 775-782
    • Bertrandy, S.1    Burlet, P.2    Clermont, O.3    Huber, C.4    Fondrat, C.5    Thierry-Mieg, D.6    Munnich, A.7    Lefebvre, S.8
  • 6
    • 1942422617 scopus 로고    scopus 로고
    • Pattern recognition strategies for molecular surfaces: III Binding site prediction with a neural network
    • Keil, M., Exner, T.E. and Brickmann, J. (2004) Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. J. Comput. Chem., 25, 779-789.
    • (2004) J. Comput. Chem , vol.25 , pp. 779-789
    • Keil, M.1    Exner, T.E.2    Brickmann, J.3
  • 7
    • 18244362861 scopus 로고    scopus 로고
    • A neural network method for identification of RNA-interacting residues in protein
    • Jeong, E., Chung, I. and Miyano, S. (2004) A neural network method for identification of RNA-interacting residues in protein. Genome Inform. Ser. Workshop Genome Inform., 15, 105-116.
    • (2004) Genome Inform. Ser. Workshop Genome Inform , vol.15 , pp. 105-116
    • Jeong, E.1    Chung, I.2    Miyano, S.3
  • 9
    • 71749114914 scopus 로고    scopus 로고
    • Exploiting structural and topological information to improve prediction of RNA-protein binding sites
    • Maetschke, S.R. and Yuan, Z. (2009) Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics, 10, 341.
    • (2009) BMC Bioinformatics , vol.10 , pp. 341
    • Maetschke, S.R.1    Yuan, Z.2
  • 11
    • 33747828217 scopus 로고    scopus 로고
    • BindN: A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
    • Wang, L. and Brown, S.J. (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-W248.
    • (2006) Nucleic Acids Res , vol.34
    • Wang, L.1    Brown, S.J.2
  • 12
    • 57649181721 scopus 로고    scopus 로고
    • Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
    • Cheng, C.W., Su, E.C., Hwang, J.K., Sung, T.Y. and Hsu, W.L. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics, 9, S6.
    • (2008) BMC Bioinformatics , vol.9
    • Cheng, C.W.1    Su, E.C.2    Hwang, J.K.3    Sung, T.Y.4    Hsu, W.L.5
  • 13
    • 40549105098 scopus 로고    scopus 로고
    • Prediction of RNA binding sites in a protein using SVM and PSSM profile
    • Kumar, M., Gromiha, M.M. and Raghava, G. (2008) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins Struct. Funct. Bioinf., 71, 189-194.
    • (2008) Proteins Struct. Funct. Bioinf , vol.71 , pp. 189-194
    • Kumar, M.1    Gromiha, M.M.2    Raghava, G.3
  • 14
    • 49749109156 scopus 로고    scopus 로고
    • PRINTR: Prediction of RNA binding sites in proteins using SVM and profiles
    • Wang, Y., Xue, Z., Shen, G. and Xu, J. (2008) PRINTR: prediction of RNA binding sites in proteins using SVM and profiles. Amino Acids, 35, 295-302.
    • (2008) Amino Acids , vol.35 , pp. 295-302
    • Wang, Y.1    Xue, Z.2    Shen, G.3    Xu, J.4
  • 15
    • 78649771394 scopus 로고    scopus 로고
    • Predicting RNA-binding residues from evolutionary information and sequence conservation
    • Huang, Y.F., Chiu, L.Y., Huang, C.C. and Huang, C.K. (2010) Predicting RNA-binding residues from evolutionary information and sequence conservation. BMC Genomics, 11(Suppl. 4), S2.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 4
    • Huang, Y.F.1    Chiu, L.Y.2    Huang, C.C.3    Huang, C.K.4
  • 16
    • 77954298385 scopus 로고    scopus 로고
    • PiRaNhA: A server for the computational prediction of RNAbinding residues in protein sequences
    • Murakami, Y., Spriggs, R.V., Nakamura, H. and Jones, S. (2010) PiRaNhA: a server for the computational prediction of RNAbinding residues in protein sequences. Nucleic Acids Res., 38, W412-W416.
    • (2010) Nucleic Acids Res , vol.38
    • Murakami, Y.1    Spriggs, R.V.2    Nakamura, H.3    Jones, S.4
  • 17
    • 77953886400 scopus 로고    scopus 로고
    • BindN+for accurate prediction of DNA and RNA-binding residues from protein sequence features
    • Wang, L., Huang, C., Yang, M. and Yang, J. (2010) BindN+for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst. Biol., 4, S3.
    • (2010) BMC Syst. Biol , vol.4
    • Wang, L.1    Huang, C.2    Yang, M.3    Yang, J.4
  • 18
    • 78650079128 scopus 로고    scopus 로고
    • Predicting RNA-binding sites in proteins using the interaction propensity of amino acid triplets
    • Yun, M.R., Byun, Y. and Han, K. (2010) Predicting RNA-binding sites in proteins using the interaction propensity of amino acid triplets. Protein Pept Lett., 17, 1102-1110.
    • (2010) Protein Pept Lett , vol.17 , pp. 1102-1110
    • Yun, M.R.1    Byun, Y.2    Han, K.3
  • 19
    • 84864053540 scopus 로고    scopus 로고
    • Prediction of RNA-binding amino acids from protein and RNA sequences
    • Choi, S. and Han, K. (2011) Prediction of RNA-binding amino acids from protein and RNA sequences. BMC Bioinformatics, 13(Suppl.), S7.
    • (2011) BMC Bioinformatics , vol.13 , Issue.SUPPL.
    • Choi, S.1    Han, K.2
  • 20
    • 77954185426 scopus 로고    scopus 로고
    • Prediction of protein-RNA binding sites by a random forest method with combined features
    • Liu, Z.P., Wu, L.Y., Wang, Y., Zhang, X.S. and Chen, L. (2010) Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, 26, 1616-1622.
    • (2010) Bioinformatics , vol.26 , pp. 1616-1622
    • Liu, Z.P.1    Wu, L.Y.2    Wang, Y.3    Zhang, X.S.4    Chen, L.5
  • 21
    • 79952487629 scopus 로고    scopus 로고
    • Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
    • Ma, X., Guo, J., Wu, J., Liu, H., Yu, J., Xie, J. and Sun, X. (2011) Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins, 79, 1230-1239.
    • (2011) Proteins , vol.79 , pp. 1230-1239
    • Ma, X.1    Guo, J.2    Wu, J.3    Liu, H.4    Yu, J.5    Xie, J.6    Sun, X.7
  • 22
    • 77954247239 scopus 로고    scopus 로고
    • NAPS: A residue-level nucleic acid-binding prediction server
    • Carson, M.B., Langlois, R. and Lu, H. (2010) NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res., 38, W431-W435.
    • (2010) Nucleic Acids Res , vol.38
    • Carson, M.B.1    Langlois, R.2    Lu, H.3
  • 23
    • 40849095892 scopus 로고    scopus 로고
    • RISP: A web-based server for prediction of RNA-binding sites in proteins
    • Tong, J., Jiang, P. and Lu, Z.H. (2008) RISP: a web-based server for prediction of RNA-binding sites in proteins. Comput. Methods Programs Biomed., 90, 148-153.
    • (2008) Comput. Methods Programs Biomed , vol.90 , pp. 148-153
    • Tong, J.1    Jiang, P.2    Lu, Z.H.3
  • 24
    • 41149087805 scopus 로고    scopus 로고
    • Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    • Chen, Y.C. and Lim, C. (2008) Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 36, e29.
    • (2008) Nucleic Acids Res , vol.36
    • Chen, Y.C.1    Lim, C.2
  • 25
    • 77949343955 scopus 로고    scopus 로고
    • Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins
    • Perez-Cano, L. and Fernandez-Recio, J. (2010) Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins, 78, 25-35.
    • (2010) Proteins , vol.78 , pp. 25-35
    • Perez-Cano, L.1    Fernandez-Recio, J.2
  • 26
    • 33845865515 scopus 로고    scopus 로고
    • Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction
    • Kim, O.T.P., Yura, K. and Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res., 34, 6450-6460.
    • (2006) Nucleic Acids Res , vol.34 , pp. 6450-6460
    • Kim, O.T.P.1    Yura, K.2    Go, N.3
  • 27
    • 79955638463 scopus 로고    scopus 로고
    • Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
    • Zhao, H., Yang, Y. and Zhou, Y. (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res., 39, 3017-3025.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3017-3025
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 28
    • 58749108303 scopus 로고    scopus 로고
    • Common physical basis of macromolecule-binding sites in proteins
    • Chen, Y.C. and Lim, C. (2008) Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res., 36, 7078-7087.
    • (2008) Nucleic Acids Res , vol.36 , pp. 7078-7087
    • Chen, Y.C.1    Lim, C.2
  • 29
    • 23144448512 scopus 로고    scopus 로고
    • ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures
    • Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, 299-302.
    • (2005) Nucleic Acids Res , vol.33 , pp. 299-302
    • Landau, M.1    Mayrose, I.2    Rosenberg, Y.3    Glaser, F.4    Martz, E.5    Pupko, T.6    Ben-Tal, N.7
  • 30
    • 84864476751 scopus 로고    scopus 로고
    • DRbind: A web server for predicting DNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    • Chen, Y.C., Wright, J.D. and Lim, C. (2012) DR.bind: a web server for predicting DNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 1-8.
    • (2012) Nucleic Acids Res , pp. 1-8
    • Chen, Y.C.1    Wright, J.D.2    Lim, C.3
  • 32
    • 13444272079 scopus 로고    scopus 로고
    • The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
    • Pearl, F., Todd, A., Sillitoe, I., Dibley, M., Redfern, O., Lewis, T., Bennett, C., Marsden, R., Grant, A., Lee, D. et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res., 33, D247-D251.
    • (2005) Nucleic Acids Res , vol.33
    • Pearl, F.1    Todd, A.2    Sillitoe, I.3    Dibley, M.4    Redfern, O.5    Lewis, T.6    Bennett, C.7    Marsden, R.8    Grant, A.9    Lee, D.10
  • 33
    • 57049150788 scopus 로고    scopus 로고
    • The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures
    • Goldenberg, O., Erez, E., Nimrod, G. and Ben-Tal, N. (2009) The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res., 37, D323-D327.
    • (2009) Nucleic Acids Res , vol.37
    • Goldenberg, O.1    Erez, E.2    Nimrod, G.3    Ben-Tal, N.4
  • 34
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor, W.R. and Orengo, C.A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
    • (1989) J. Mol. Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 35
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 36
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 37
    • 0028961335 scopus 로고
    • SCOP: A structural classification of protein database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of protein database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 38
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 39
    • 84862671752 scopus 로고    scopus 로고
    • Local structural differences in homologous proteins: Specificities in different SCOP classes
    • Joseph, A.P., Valadie?H., Srinivasan, N. and de Brevern, A.G. (2012) Local structural differences in homologous proteins: specificities in different SCOP classes. PLoS One, 7, e38805.
    • (2012) PLoS One , vol.7
    • Joseph, A.P.1    Valadie, H.2    Srinivasan, N.3    De Brevern, A.G.4
  • 41
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu, A.A., Shelenkov, A.A. and Dunbrack, R.L. Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 43
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T. et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem., 24, 1999-2012.
    • (2003) J. Comput. Chem , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10
  • 44
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E. and Ben-Tal, N. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 45
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces cavities, and intermolecular interactions
    • Laskowski, R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330.
    • (1995) J. Mol. Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 46
    • 77649142047 scopus 로고    scopus 로고
    • Multiple structure alignment and consensus identification for proteins
    • Ilinkin, I., Ye, J. and Janardan, R. (2010) Multiple structure alignment and consensus identification for proteins. BMC Bioinformatics, 11, 71.
    • (2010) BMC Bioinformatics , vol.11 , pp. 71
    • Ilinkin, I.1    Ye, J.2    Janardan, R.3
  • 48
    • 84866900058 scopus 로고    scopus 로고
    • NMDAR signaling facilitates the IPO5-mediated nuclear import of CPEB3
    • Chao, H.W., Lai, Y.T., Lu, Y.L., Lin, C.L., Mai, W. and Huang, Y.S. (2012) NMDAR signaling facilitates the IPO5-mediated nuclear import of CPEB3. Nucleic Acids Res., 40, 8484-8498.
    • (2012) Nucleic Acids Res , vol.40 , pp. 8484-8498
    • Chao, H.W.1    Lai, Y.T.2    Lu, Y.L.3    Lin, C.L.4    Mai, W.5    Huang, Y.S.6
  • 49
    • 34247250713 scopus 로고    scopus 로고
    • Predicting DNA-binding sites on proteins from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation
    • Chen, Y.C., Wu, C.Y. and Lim, C. (2007) Predicting DNA-binding sites on proteins from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins Struct. Funct. Bioinf., 67, 671-680.
    • (2007) Proteins Struct. Funct. Bioinf , vol.67 , pp. 671-680
    • Chen, Y.C.1    Wu, C.Y.2    Lim, C.3


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