Prediction of RNA-binding amino acids from protein and RNA sequences

BMC Bioinformatics

Volumn 12, Issue SUPPL. 13, 2011, Pages

  Choi, Sungwook ^a   Han, Kyungsook ^a  

^a Inha University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BETTER PERFORMANCE; CORRELATION COEFFICIENT; CROSS VALIDATION; DATA REDUNDANCY; F-MEASURE; FEATURE VECTORS; GLOBAL FEATURE; INTERACTION SITE; LEARNING APPROACH; LEARNING MODELS; NON-REDUNDANT; PROTEIN BINDS; PROTEIN FEATURES; PROTEIN SEQUENCES; REDUNDANCY REDUCTIONS; REDUNDANT DATA; RNA BINDING; RNA SEQUENCES; RNA-BINDING RESIDUES; SEQUENCE SIMILARITY; SIMILARITY-BASED METHODS; SVM MODEL; TRAINING DATASET; VECTOR-BASED METHODS;

AMINO ACIDS; FORECASTING; IMAGE RETRIEVAL; PROTEINS; STATISTICAL TESTS; SUPPORT VECTOR MACHINES;

RNA;

AMINO ACID; NUCLEOTIDE; RNA; RNA BINDING PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; SUPPORT VECTOR MACHINE;

AMINO ACIDS; BINDING SITES; MODELS, MOLECULAR; NUCLEOTIDES; RNA; RNA-BINDING PROTEINS; SUPPORT VECTOR MACHINES;

EID: 84864053540     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S13-S7     Document Type: Article

References (15)

1. Draper DE. Protein-RNA recognition. Annu. Rev. Biochem 1995, 64:593-620. 10.1146/annurev.bi.64.070195.003113, 7574494.
2. 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, 34:W243-W248. 10.1093/nar/gkl298, 1538853, 16845003.
3. 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. 10.1261/rna.2197306, 1524891, 16790841.
4. 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, 35:578-584.
5. Kim H, Jeong E, Lee SW, Han K. Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Letters 2003, 552:231-239. 10.1016/S0014-5793(03)00930-X, 14527692.
6. Han K, Nepal C. PRI-Modeler: Extracting RNA structural elements from PDB files of protein-RNA complexes. FEBS Letters 2007, 581:1881-1890. 10.1016/j.febslet.2007.03.085, 17434486.
7. Yun MR, Byun Y, Han K. Predicting RNA-binding sites in proteins using the interaction propensity of amino acid triplets. Protein and Peptide Letters 2010, 17:1102-1110. 10.2174/092986610791760388, 20509851.
8. Cheng CW, Su EC, Hwang JK, Sung TY, Hsu WL. Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics 2008, 9(Suppl 12):S6. 10.1186/1471-2105-9-S12-S6, 2638146, 19091029.
9. Kumar M, Gromiha MM, Raghava GP. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins 2008, 71:189-194. 10.1002/prot.21677, 17932917.
10. Liu ZP, Wu LY, Wang Y, Zhang XS, Chen L. Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics 2010, 26:1616-1622. 10.1093/bioinformatics/btq253, 20483814.
11. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26:680-682. 10.1093/bioinformatics/btq003, 2828112, 20053844.
12. Shrestha R, Kim J, Han K. Prediction of RNA-binding residues in proteins using the interaction propensities of amino acids and nucleotides. LNCS 2008, 5226:114-121.
13. Torshine IY, Weber IT, Harrison RW. Geometric criteria of hydrogen bonds in proteins and identification of 'bifurcated' hydrogen bonds. Protein Engineering 2002, 15:359-363. 10.1093/protein/15.5.359, 12034855.
14. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16:412-424. 10.1093/bioinformatics/16.5.412, 10871264.
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.