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Adaptive Simulated Annealing and its Application to Protein Folding

ASA

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Encyclopedia of Optimization

Article Outline

Keywords

The ASA Method

  Monte-Carlo Configurations

  Annealing Schedule

  Re-Annealing

Application to Protein Folding

  Computational Details

  Met-Enkephalin

  Poly(L-Alanine)

Conclusion

Recent Studies and Future Directions

See also

References

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References

  1. Gay DM (1983) Subroutines for unconstrained minimization using a model/trust-region approach. ACM Trans Math Softw 9:503

    MathSciNet  MATH  Google Scholar 

  2. Hansmann UHE (1998) Generalized ensembles: A new way of simulating proteins. Phys A 254:15

    Google Scholar 

  3. Ingber L (1989) Very fast simulated re-annealing. Math Comput Modelling 12:967 ASA code is available from: ftp.alumni.caltech.edu:pub/ingber

    MathSciNet  MATH  Google Scholar 

  4. Ingber L, Rosen B (1992) Genetic algorithm and very fast simulated re-annealing: A comparison. Math Comput Modelling 16:87

    MathSciNet  MATH  Google Scholar 

  5. Jin AY, Leung FY, Weaver DF (1997) Development of a novel genetic algorithm search method (GAP1.0) for exploring peptide conformational space. J Comput Chem 18:1971

    Google Scholar 

  6. Kirkpatrick S, Gelatt CD, Vecchi MP Jr (1983) Optimization by simulated annealing. Science 220:671

    MathSciNet  Google Scholar 

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

    Google Scholar 

  8. Li Z, Scheraga HA (1987) Monte Carlo-minimization approach to the multiminima problem in protein folding. Proc Nat Aca Sci USA 84:6611

    MathSciNet  Google Scholar 

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

    Google Scholar 

  10. Merkle LD, Lamont GB, Gates GH, Pachter R (May, 1996) Hybrid genetic algorithms for minimization of polypeptide specific energy model. Proc. IEEE Int. Conf. Evolutionary Computation, p 192

    Google Scholar 

  11. Nayeem A, Vila J, Scheraga HA (1991) 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 12:594

    Google Scholar 

  12. Okamoto Y, Kikuchi T, Kawai H (1992) Prediction of low-energy structure of Met-Enkephalin by Monte Carlo simulated annealing. Chem Lett (Chem Soc Japan):1275

    Google Scholar 

  13. Piela L, Scheraga HA (1987) On the multiple-minima problem in the conformational analysis of polypeptides: I. backbone degrees of freedom for a perturbed α-helix. Biopolymers 26:S33

    Google Scholar 

  14. Vasquez M (1999) Private communication

    Google Scholar 

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

    Google Scholar 

  16. Wilson SR, Cui W (1990) Applications of simulated annealing to peptides. Biopolymers 29:225

    Google Scholar 

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Author information

Authors and Affiliations

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

    Ruth Pachter & Zhiqiang Wang

Authors
  1. Ruth Pachter
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  2. Zhiqiang Wang
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Editor information

Editors and Affiliations

  1. Department of Chemical Engineering, Princeton University, Princeton, NJ, 08544-5263, USA

    Christodoulos A. Floudas

  2. Center for Applied Optimization, Department of Industrial and Systems Engineering, University of Florida, Gainesville, FL, 32611-6595, USA

    Panos M. Pardalos

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© 2008 Springer-Verlag

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Pachter, R., Wang, Z. (2008). Adaptive Simulated Annealing and its Application to Protein Folding . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_5

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