publication . Article . 2008

Predicting RNA-binding sites of proteins using support vector machines and evolutionary information

Cheng-Wei Cheng;
Open Access
  • Published: 01 Dec 2008 Journal: BMC Bioinformatics, volume 9, page S6 (issn: 1471-2105, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
<p>Abstract</p> <p>Background</p> <p>RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding sites in proteins provides valuable insights for biologists. However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. Extensive studies of RNA-binding site prediction have led to the development of several methods. However, they could yield low sensitivities in tra...
Subjects
free text keywords: Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Research
23 references, page 1 of 2

Sunita, S, Purta, E, Durawa, M, Tkaczuk, KL, Swaathi, J, Bujnicki, JM, Sivaraman, J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res. 2007; 35: 4264-4274 [OpenAIRE] [PubMed] [DOI]

Bechara, E, Davidovic, L, Melko, M, Bensaid, M, Tremblay, S, Grosgeorge, J, Khandjian, EW, Lalli, E, Bardoni, B. Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure. Nucleic Acids Res. 2007; 35: 299-306 [OpenAIRE] [PubMed] [DOI]

McKnight, KL, Heinz, BA. RNA as a target for developing antivirals. Antivir Chem Chemother. 2003; 14: 61-73 [PubMed]

Berman, HM, Battistuz, T, Bhat, TN, Bluhm, WF, Bourne, PE, Burkhardt, K, Feng, Z, Gilliland, GL, Iype, L, Jain, S. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002; 58: 899-907 [OpenAIRE] [PubMed] [DOI]

Jeong, E, Chung, IF, Miyano, S. A neural network method for identification of RNA-interacting residues in protein. Genome Inform. 2004; 15: 105-116 [PubMed]

Terribilini, M, Lee, JH, Yan, C, Jernigan, RL, Honavar, V, Dobbs, D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA. 2006; 12: 1450-1462 [OpenAIRE] [PubMed] [DOI]

Jeong, E, Miyano, S. A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction. Transactions on Computational Systems Biology. 2006: 123-139

Kumar, M, Gromiha, MM, Raghava, GP. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins. 2008; 71: 189-194 [OpenAIRE] [PubMed] [DOI]

Wang, L, Brown, SJ. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res. 2006: W243-248 [OpenAIRE] [PubMed] [DOI]

Gonzalez, RC, Woods, RE. Digital Image Processing. 2002

Terribilini, M, Sander, JD, Lee, JH, Zaback, P, Jernigan, RL, Honavar, V, Dobbs, D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007: W578-584 [OpenAIRE] [PubMed] [DOI]

Vapnik, VN. The Nature of Statistical Learning Theory. 1995 [PubMed]

LIBSVM: a library for support vector machines.

Altschul, SF, Madden, TL, Schaffer, AA, Zhang, J, Zhang, Z, Miller, W, Lipman, DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389-3402 [OpenAIRE] [PubMed] [DOI]

Henikoff, S, Henikoff, JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA. 1992; 89: 10915-10919 [OpenAIRE] [PubMed] [DOI]

23 references, page 1 of 2
Abstract
<p>Abstract</p> <p>Background</p> <p>RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding sites in proteins provides valuable insights for biologists. However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. Extensive studies of RNA-binding site prediction have led to the development of several methods. However, they could yield low sensitivities in tra...
Subjects
free text keywords: Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Research
23 references, page 1 of 2

Sunita, S, Purta, E, Durawa, M, Tkaczuk, KL, Swaathi, J, Bujnicki, JM, Sivaraman, J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res. 2007; 35: 4264-4274 [OpenAIRE] [PubMed] [DOI]

Bechara, E, Davidovic, L, Melko, M, Bensaid, M, Tremblay, S, Grosgeorge, J, Khandjian, EW, Lalli, E, Bardoni, B. Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure. Nucleic Acids Res. 2007; 35: 299-306 [OpenAIRE] [PubMed] [DOI]

McKnight, KL, Heinz, BA. RNA as a target for developing antivirals. Antivir Chem Chemother. 2003; 14: 61-73 [PubMed]

Berman, HM, Battistuz, T, Bhat, TN, Bluhm, WF, Bourne, PE, Burkhardt, K, Feng, Z, Gilliland, GL, Iype, L, Jain, S. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002; 58: 899-907 [OpenAIRE] [PubMed] [DOI]

Jeong, E, Chung, IF, Miyano, S. A neural network method for identification of RNA-interacting residues in protein. Genome Inform. 2004; 15: 105-116 [PubMed]

Terribilini, M, Lee, JH, Yan, C, Jernigan, RL, Honavar, V, Dobbs, D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA. 2006; 12: 1450-1462 [OpenAIRE] [PubMed] [DOI]

Jeong, E, Miyano, S. A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction. Transactions on Computational Systems Biology. 2006: 123-139

Kumar, M, Gromiha, MM, Raghava, GP. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins. 2008; 71: 189-194 [OpenAIRE] [PubMed] [DOI]

Wang, L, Brown, SJ. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res. 2006: W243-248 [OpenAIRE] [PubMed] [DOI]

Gonzalez, RC, Woods, RE. Digital Image Processing. 2002

Terribilini, M, Sander, JD, Lee, JH, Zaback, P, Jernigan, RL, Honavar, V, Dobbs, D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007: W578-584 [OpenAIRE] [PubMed] [DOI]

Vapnik, VN. The Nature of Statistical Learning Theory. 1995 [PubMed]

LIBSVM: a library for support vector machines.

Altschul, SF, Madden, TL, Schaffer, AA, Zhang, J, Zhang, Z, Miller, W, Lipman, DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389-3402 [OpenAIRE] [PubMed] [DOI]

Henikoff, S, Henikoff, JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA. 1992; 89: 10915-10919 [OpenAIRE] [PubMed] [DOI]

23 references, page 1 of 2
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