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Simulated Annealing Methods in Protein Folding

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Encyclopedia of Optimization

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References

  1. Alemany PA, Zanette DH (1994) Fractal random walks from a variational formalism for Tsallis entropies. Phys Rev E 49:R956–R958

    Article  Google Scholar 

  2. Andricioaei I, Straub JE (1996) Generalized simulated annealing algorithm using Tsallis statistics: Application to conformational optimization of a tetrapeptide. Phys Rev E 53:R3055–R3058

    Article  Google Scholar 

  3. Andricioaei I, Straub JE (1998) Global optimization using bad derivatives: A derivative-free method for molecular energy minimization. J Comput Chem 19:1445–1455

    Article  Google Scholar 

  4. Bachas CP (1984) Computer-intractability of the frustration model of a spin glass. J Phys A: Math Gen 17:L709–L712

    Article  MathSciNet  Google Scholar 

  5. Brooks III CL, Karplus M, Montgomery Pettitt B (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. Wiley, New York

    Google Scholar 

  6. Frenkel D, Smit B (1996) Understanding molecular simulation: From algorithms to applications. Acad. Press, New York

    MATH  Google Scholar 

  7. Gibson KD, Scheraga HA (1988) The multiple-minima problem in protein folding. In: Sarma MH, Sarma RH (eds) Structure and Expression: From Proteins to Ribosomes, vol 1. Adenine Press, Schenectady, NY

    Google Scholar 

  8. Hansmann UHE, Okamoto Y (1998) Stochastic dynamics simulations in a new generalized ensemble. Chem Phys Lett 297:374–382

    Article  Google Scholar 

  9. Kirkpatrick S, Gelatt CD, Vecchi MP (1989) Optimization by simulated annealing. Science 220:671–680

    Article  MathSciNet  Google Scholar 

  10. Kostrowicki J, Piela L, Cherayil BJ, Scheraga HA (1991) Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard–Jones atoms. J Phys Chem 95:4113–4119; Kostrowicki J, Scheraga HA (1992) J Phys Chem 96:7442–7449

    Article  Google Scholar 

  11. Ma J, Straub JE (1994) Simulated annealing using the classical density distribution. J Chem Phys 101:533–541; ibid (1995) 103:9113–9113

    Article  Google Scholar 

  12. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092

    Article  Google Scholar 

  13. Ngo JT, Marks J, Karplus M (1994) Computational complexity, protein structure prediction, and the Levinthal paradox. In: Merz K, LeGrand S (eds) The protein folding problem and tertiary structure prediction. Birkhäuser, Basel, pp 433–506

    Google Scholar 

  14. Okamoto Y (1998) Protein folding problem as studied by new simulation algorithms. Recent Res Developm Pure Appl Chem 2:1–22

    Google Scholar 

  15. Orešič M, Shalloway D (1994) Hierarchical characterization of energy landscapes using Gaussian packet states. J Chem Phys 101:9844–9857

    Article  Google Scholar 

  16. Pangali C, Rao M, Berne BJ (1978) On a novel Monte Carlo scheme for simulating water and aqueous solutions. Chem Phys Lett 55:413–417

    Article  Google Scholar 

  17. Roitberg A, Elber R (1991) Modeling side chains in peptides and proteins: Application of the Locally Enhanced Sampling (LES) and the simulated annealing methods to find minimum energy conformations. J Chem Phys 95:9277–9287

    Article  Google Scholar 

  18. Rossky PJ, Doll JD, Friedman HL (1978) Brownian dynamics as smart Monte Carlo simulation. J Chem Phys 69:4628–4633

    Article  Google Scholar 

  19. Stariolo DA, Tsallis C (1995) Optimization by simulated annealing: Recent progress. In: Stauffer D (ed) Anual Reviews of Computational Physics II. World Sci., Singapore p 343

    Google Scholar 

  20. Straub JE (1996) Optimization techniques with applications to proteins. In: Elber R (ed) New Developments in Theoretical Studies of Proteins. World Sci., Singapore, pp 137–196

    Google Scholar 

  21. Straub JE, Andricioaei I (1998) Exploiting Tsallis statistics. In: Deuflhard P, Hermans J, Leimkuhler B, Mark A, Reich S, Skeel RD (eds) Algorithms for Macromolecular Modelling. Lecture Notes Computational Sci and Engin. Springer, Berlin, pp 189–204

    Google Scholar 

  22. Szu H, Hartley R (1987) Fast simulated annealing. Phys Lett A 122:157–162

    Article  Google Scholar 

  23. Tsoo C, Brooks III CL (1994) Cluster structure determination using Gaussian density distribution global minimization methods. J Chem Phys 101:6405–6411

    Article  Google Scholar 

  24. Wille LT, Vennik J (1985) Computational complexity of the ground-state determination of atomic clusters. J Phys A: Math Gen 18:L419–L422

    Article  MathSciNet  Google Scholar 

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Author information

Authors and Affiliations

  1. Boston University, Boston, USA

    Ioan Andricioaei & John Straub

Authors
  1. Ioan Andricioaei
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  2. John Straub
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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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Andricioaei, I., Straub, J. (2008). Simulated Annealing Methods in Protein Folding . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_618

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