메뉴 건너뛰기




Volumn , Issue , 2004, Pages 223-230

A parallel evolutionary algorithm for RNA secondary structure prediction using stacking-energies (INN and INN-HB)

Author keywords

Genetic algorithms; RNA; Stacking energy; Structure prediction

Indexed keywords

FREE ENERGY; GENETIC ALGORITHMS; HYDROGEN BONDS; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 17044414373     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (7)

References (37)
  • 2
    • 0031431078 scopus 로고    scopus 로고
    • RNA crystallography
    • S. R. Holbrook and S.-H. Kim, "RNA Crystallography," in Biopolymers, vol. 44, pp. 3-21, 1997.
    • (1997) Biopolymers , vol.44 , pp. 3-21
    • Holbrook, S.R.1    Kim, S.-H.2
  • 4
    • 0345281589 scopus 로고    scopus 로고
    • How RNA folds
    • Oct.
    • I. Tinoco Jr. and C. Bustamante, "How RNA Folds," in J. Mol. Biol., vol. 293(N2),pp. 271-281, Oct. 1999.
    • (1999) J. Mol. Biol. , vol.293 , Issue.N2 , pp. 271-281
    • Tinoco Jr., I.1    Bustamante, C.2
  • 5
    • 0003251874 scopus 로고    scopus 로고
    • RNA secondary structure prediction
    • Serge L. Beaucage, Donald E. Bergstrum, Gary D. Glick, and Roger A. Jones, eds. John Wiley and Sons, Inc.
    • David H. Mathews, Douglas H. Turner, and Michael Zuker, "RNA Secondary Structure Prediction," in Current Protocols in Nucleic Acid Chemistry, Serge L. Beaucage, Donald E. Bergstrum, Gary D. Glick, and Roger A. Jones, eds. John Wiley and Sons, Inc. 11.2.1 -11.2.10, 2000.
    • (2000) Current Protocols in Nucleic Acid Chemistry
    • Mathews, D.H.1    Turner, D.H.2    Zuker, M.3
  • 6
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • May
    • J.P. Abrahams, M. van der Berg, E. van Batenburg, and C. Pleij, "Prediction of RNA secondary structure, including pseudoknotting, by computer simulation," in Nucleic Acids Research, vol 18(10), pp. 3035-44, May 1990.
    • (1990) Nucleic Acids Research , vol.18 , Issue.10 , pp. 3035-3044
    • Abrahams, J.P.1    Van Der Berg, M.2    Van Batenburg, E.3    Pleij, C.4
  • 7
    • 0002277269 scopus 로고
    • Probing RNA structure, function, and history by comparative analysis
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • C. Woese and N. Pace.,"Probing RNA structure, function, and history by comparative analysis," in The RNA World, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993.
    • (1993) The RNA World
    • Woese, C.1    Pace, N.2
  • 8
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • June
    • F. H. D. van Batenburg, A. P. Gultyaev, and C. W. A. Pleij., "An APL-programmed genetic algorithm for the prediction of RNA secondary structure," in Journal of Theoretical Biology, vol. 174, pp. 269-280, June 1995.
    • (1995) Journal of Theoretical Biology , vol.174 , pp. 269-280
    • Van Batenburg, F.H.D.1    Gultyaev, A.P.2    Pleij, C.W.A.3
  • 10
    • 0028547954 scopus 로고
    • A massively-parallel genetic algorithm for RNA secondary structure prediction
    • B. A. Shapiro, and J. Navetta, "A massively-parallel genetic algorithm for RNA secondary structure prediction," in The Journal of Supercomputing, vol. 8, pp. 195-207, 1995.
    • (1995) The Journal of Supercomputing , vol.8 , pp. 195-207
    • Shapiro, B.A.1    Navetta, J.2
  • 13
    • 0029040124 scopus 로고
    • A genetic algorithm to search for optimal and suboptimal RNA secondary structures
    • G. Benedetti and S. Morosetti, "A genetic algorithm to search for optimal and suboptimal RNA secondary structures," Biophysical Chemistry, 55, pp. 253-259, 1995.
    • (1995) Biophysical Chemistry , vol.55 , pp. 253-259
    • Benedetti, G.1    Morosetti, S.2
  • 14
    • 0345407811 scopus 로고    scopus 로고
    • A permutation based genetic algorithm for RNA secondary structure prediction
    • A. Abraham, J. Ruiz-del-Solar and M. Koppen, Eds., IOS Press, Amsterdam
    • K. C. Wiese and E. Glen, "A Permutation Based Genetic Algorithm for RNA Secondary Structure Prediction," in Frontiers in Artificial Intelligence and Applications - Soft Computing Systems, 87, A. Abraham, J. Ruiz-del-Solar and M. Koppen, Eds., IOS Press, Amsterdam, pp. 173-182, 2002.
    • (2002) Frontiers in Artificial Intelligence and Applications - Soft Computing Systems , vol.87 , pp. 173-182
    • Wiese, K.C.1    Glen, E.2
  • 15
    • 0345293275 scopus 로고    scopus 로고
    • A permutation-based genetic algorithm for the RNA folding problem: A critical look at selection strategies, crossover operators, and representation issues
    • G. Fogel and D. Come, Eds.
    • K. C. Wiese and E. Glen, "A Permutation-Based Genetic Algorithm for the RNA Folding Problem: A Critical Look at Selection Strategies, Crossover Operators, and Representation Issues", BioSystems - Special Issue on Computational Intelligence in Bioinformatics, Vol. 72 (1-2), G. Fogel and D. Come, Eds., pp. 29-41, 2003.
    • (2003) BioSystems - Special Issue on Computational Intelligence in Bioinformatics , vol.72 , Issue.1-2 , pp. 29-41
    • Wiese, K.C.1    Glen, E.2
  • 18
    • 0003875048 scopus 로고
    • A summary of research on parallel genetic algorithms
    • E. Cantú-Paz, "A Summary of Research on Parallel Genetic Algorithms," Illi-GAL, Report No. 9500, 1995.
    • (1995) Illi-GAL, Report No. 9500 , vol.9500
    • Cantú-Paz, E.1
  • 21
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • M. J. Serra, and D. H. Turner, "Predicting thermodynamic properties of RNA," Methods in Enzymology, 259, pp. 242-261, 1995.
    • (1995) Methods in Enzymology , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 22
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • T. Xia, J. SantaLucia Jr, M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, "Thermodynamic Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs" Biochemistry, 37, 14719-14735, 1998.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 23
    • 4344701951 scopus 로고    scopus 로고
    • Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - A comparison to known structures
    • A. Deschênes and K. C. Wiese, "Using Stacking-Energies (INN and INN-HB) for Improving the Accuracy of RNA Secondary Structure Prediction with an Evolutionary Algorithm - A Comparison to Known Structures," in Proceedings of the 2004 Congress on Evolutionary Computation (CEC 2004), pp. 598-606, 2004.
    • (2004) Proceedings of the 2004 Congress on Evolutionary Computation (CEC 2004) , pp. 598-606
    • Deschênes, A.1    Wiese, K.C.2
  • 24
    • 17044391204 scopus 로고    scopus 로고
    • Laboratoire de Biologie Informatique et Théorique, Universit'e de Montréal, Montréal, Canada, (personal communication)
    • F. Major, Laboratoire de Biologie Informatique et Théorique, Universit'e de Montréal, Montréal, Canada, (personal communication), 2003.
    • (2003)
    • Major, F.1
  • 25
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • D. H. Mathews, J. Sabina, M. Zuker and D. H. Turner "Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure" Journal of Molecular Biology, 288, 911-940, 1999.
    • (1999) Journal of Molecular Biology , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 26
    • 0023040885 scopus 로고
    • Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids
    • S. M. Freier, N. Sugimoto, A. Sinclair, D. Alkema, T. Neilson, R. Kierzek, M. H. Caruthers, and D. H. Turner, "Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids," Biochemistry, 25, 3214-3219, 1986.
    • (1986) Biochemistry , vol.25 , pp. 3214-3219
    • Freier, S.M.1    Sugimoto, N.2    Sinclair, A.3    Alkema, D.4    Neilson, T.5    Kierzek, R.6    Caruthers, M.H.7    Turner, D.H.8
  • 27
    • 0023040892 scopus 로고
    • Free-energy contributions of GU and other terminal mismatches to helix stability
    • S. M. Freier, R. Kierzek, M. H. Caruthers, T. Neilson, and D. H. Turner, "Free-energy contributions of GU and other terminal mismatches to helix stability" Biochemistry, 25, 3209-3213, 1986.
    • (1986) Biochemistry , vol.25 , pp. 3209-3213
    • Freier, S.M.1    Kierzek, R.2    Caruthers, M.H.3    Neilson, T.4    Turner, D.H.5
  • 28
    • 0023055766 scopus 로고
    • Energetics of internal GU mismatches in ribooligonucleotide helixes
    • N. Sugimoto, R. Kierzek, S. M. Freier, and D. H. Turner, "Energetics of internal GU mismatches in ribooligonucleotide helixes," Biochemistry, 25, pp. 5755-5759, 1986.
    • (1986) Biochemistry , vol.25 , pp. 5755-5759
    • Sugimoto, N.1    Kierzek, R.2    Freier, S.M.3    Turner, D.H.4
  • 30
    • 0028917227 scopus 로고
    • A periodic table of symmetric tandem mismatches in RNA
    • M. Wu, J. A. McDowell, and D. H. Turner, "A periodic table of symmetric tandem mismatches in RNA," Biochemistry, 34, pp. 3204-3211, 1995.
    • (1995) Biochemistry , vol.34 , pp. 3204-3211
    • Wu, M.1    McDowell, J.A.2    Turner, D.H.3
  • 31
    • 0030815643 scopus 로고    scopus 로고
    • Thermodynamics of nonsymmetric tandem mismatches adjacent to GC base pairs in RNA
    • T. Xia, J. A. McDowell, and D. H. Turner, "Thermodynamics of nonsymmetric tandem mismatches adjacent to GC base pairs in RNA" Biochemistry, 36, 12486-12487, 1997.
    • (1997) Biochemistry , vol.36 , pp. 12486-12487
    • Xia, T.1    McDowell, J.A.2    Turner, D.H.3
  • 37
    • 17044383132 scopus 로고    scopus 로고
    • Accessed: October 22nd, 2003
    • The openMosix Project, http://openmosix.sourceforge.net/Accessed: October 22nd, 2003.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.