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

10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)

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

CORRELATION COEFFICIENT; CROSS VALIDATION; DATA REDUNDANCY; DATA SETS; F-MEASURE; FEATURE VECTORS; GLOBAL FEATURE; INTERACTION SITE; LEARNING APPROACH; LEARNING MODELS; PROTEIN BINDS; PROTEIN SEQUENCES; REDUCTION METHOD; REDUNDANT DATA; RNA BINDING; RNA MOLECULES; RNA SEQUENCES; RNA-BINDING RESIDUES; SEQUENCE SIMILARITY; SIMILARITY-BASED METHODS; SVM MODEL; TRAINING DATASET; VECTOR-BASED METHODS;

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

RNA;

EID: 84871869026     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (15)

1. Draper DE: Protein-RNA recognition. Annu. Rev. Biochem 1995, 64:593-620.
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. (Pubitemid 44529772)
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. (Pubitemid 44141524)
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. (Pubitemid 37186866)
6. Han K, Nepal C: PRI-Modeler: Extracting RNA structural elements from PDB files of protein-RNA complexes. FEBS Letters 2007, 581:1881-1890. (Pubitemid 46602285)
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.
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.
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. (Pubitemid 351358602)
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.
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.
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. (Pubitemid 34601727)
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. (Pubitemid 30487963)
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov ININ, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. (Pubitemid 30047768)