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Adaptive Simulated Annealing and its Application to Protein Folding

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References

  1. Gay, D.M.: ‘Subroutines for unconstrained minimization using a model/trust-region approach’, ACM Trans. Math. Software9 (1983), 503.

    MathSciNet  MATH  Google Scholar 

  2. Hansmann, U.H.E.: ‘Generalized ensembles: A new way of simulating proteins’, Phys. A254 (1998), 15.

    Google Scholar 

  3. Ingber, L.: ‘Very fast simulated re-annealing’, Math. Comput. Modelling12 (1989), 967 ASA code is available from: ftp.alumni.caltech.edu:pub/ingber.

    MathSciNet  MATH  Google Scholar 

  4. Ingber, L., and Rosen, B.: ‘Genetic algorithm and very fast simulated re-annealing: A comparison’, Math. Comput. Modelling16 (1992), 87.

    MathSciNet  MATH  Google Scholar 

  5. Jin, A.Y., Leung, F.Y., and Weaver, D.F.: ‘Development of a novel genetic algorithm search method (GAP1.0) for exploring peptide conformational space’, J. Comput. Chem.18 (1997), 1971.

    Google Scholar 

  6. Kirkpatrick, S., Gelatt, C.D., and Vecchi Jr., M.P.: ‘Optimization by simulated annealing’, Science220 (1983), 671.

    MathSciNet  Google Scholar 

  7. Lee, J., Scheraga, H.A., and Rackovsky, S.: ‘New optimization method for conformational energy calculations on polypeptides: conformational space annealing’, J. Comput. Chem.18 (1997), 222.

    Google Scholar 

  8. Li, Z., and Scheraga, H.A.: ‘Monte Carlo-minimization approach to the multiminima problem in protein folding’, Proc. Nat. Aca. Sci. USA84 (1987), 6611.

    MathSciNet  Google Scholar 

  9. Li, Z., and Scheraga, H.A.: ‘Structure and free energy of complex thermodynamic systems’, J. Mol. Struct. (Theochem)179 (1988), 333.

    Google Scholar 

  10. Merkle, L.D., Lamont, G.B., Gates, G.H., and Pachter, R.: ‘Hybrid genetic algorithms for minimization of polypeptide specific energy model’, Proc. IEEE Internat. Conf. Evolutionary Computation, May, 1996 p. 192.

    Google Scholar 

  11. Nayeem, A., Vila, J., and Scheraga, H.A.: ‘A comparative study of the simulated-annealing and Monte Carlo-with minimization approaches to the minimum-energy structures of polypeptides: Met-Enkephalin’, J. Comput. Chem.12 (1991), 594.

    Google Scholar 

  12. Okamoto, Y., Kikuchi, T., and Kawai, H.: ‘Prediction of low-energy structure of Met-Enkephalin by Monte Carlo simulated annealing’, Chem. Lett. (Chem. Soc. Japan) (1992), 1275.

    Google Scholar 

  13. Piela, L., and Scheraga, H.A.: ‘On the multiple-minima problem in the conformational analysis of polypeptides: I. backbone degrees of freedom for a perturbed α-helix’, Biopolymers26 (1987), S33.

    Google Scholar 

  14. Vasquez, M.: Private communication (1999).

    Google Scholar 

  15. Wang, Z., and Pachter, R.: ‘Prediction of polypeptide conformation by the adaptive simulated annealing approach’, J. Comput. Chem.18 (1997), 323.

    Google Scholar 

  16. Wilson, S.R., and Cui, W.: ‘Applications of simulated annealing to peptides’, Biopolymers29 (1990), 225.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Air Force Research Laboratory Materials & Manufacturing Directorate Wright–Patterson AFB, Dayton, OH, 45433–7702, USA

    Ruth Pachter

  2. Air Force Research Laboratory Materials & Manufacturing Directorate Wright–Patterson AFB, Dayton, OH, 45433–7702, USA

    Zhiqiang Wang

Authors
  1. Ruth Pachter
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  2. Zhiqiang Wang
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Editor information

Editors and Affiliations

  1. Dept. Chemical Engin., Princeton Univ., Princeton, NJ, 08544-5263, USA

    Christodoulos A. Floudas

  2. Center for Applied Optim. Dept. Industrial and Systems Engin., Univ. Florida, Gainesville, FL, 32611, USA

    Panos M. Pardalos

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© 2001 Kluwer Academic Publishers

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Pachter, R., Wang, Z. (2001). Adaptive Simulated Annealing and its Application to Protein Folding . In: Floudas, C.A., Pardalos, P.M. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/0-306-48332-7_5

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  • DOI: https://doi.org/10.1007/0-306-48332-7_5

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-7923-6932-5

  • Online ISBN: 978-0-306-48332-5

  • eBook Packages: Springer Book Archive

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