Global Optimization of Morse Clusters by Potential Energy Transformations

Published Online:https://doi.org/10.1287/ijoc.1040.0084

References

  • Abkevich V. I., Gutin A. M., Shakhnovich E. I. Free energy landscape for protein folding kinetics: Intermediates, traps and multiple pathways in theory and lattice model simulations. J. Chem. Phys. (1994) 101:6052–6062CrossrefGoogle Scholar
  • Addis B., Schoen F. A randomized global optimization method for protein-protein docking. (2003) . Technical report DSI 4-2003, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Firenze, ItalyGoogle Scholar
  • Bryngelson J. D, Onuchic J. N., Socci N. D., Wolynes P. G. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins (1995) 21:167–195CrossrefGoogle Scholar
  • Doye J. P. K. The effect of compression on the global optimization of atomic clusters. Phys. Rev. E (2000) 62:8753–8761CrossrefGoogle Scholar
  • Doye J. P. K., Wales D. J. Structural consequences of the range of the interatomic potential: A menagerie of clusters. J. Chem. Soc. Faraday Trans. (1997) 93:4233–4244CrossrefGoogle Scholar
  • Doye J. P. K., Wales D. J. Thermodynamics of global optimization. Phys. Rev. Lett. (1998) 80:1357–1360CrossrefGoogle Scholar
  • Doye J. P. K., Miller M. A., Wales D. J. Evolution of the potential energy surface with size for Lennard-Jones clusters. J. Chem. Phys. (1999) 111(18):8417–8428CrossrefGoogle Scholar
  • Doye J. P. K., Wales D. J., Simdyankin S. I. Global optimization and the energy landscapes of Dzugutov clusters. Faraday Discuss (2001a) 118:159–170CrossrefGoogle Scholar
  • Doye J. P. K., Wales D. J., Branz W., Calvo F. Modelling the structure of C60 clusters. Phys. Rev. B (2001b) 64:1–11CrossrefGoogle Scholar
  • Guo Z. Y., Thirumalai D. Kinetics of protein-folding—Nucleation mechanism, time scales, and pathways. Biopolymers (1995) 36:83–102CrossrefGoogle Scholar
  • Kiefhaber T. Kinetic traps in lysozyme folding. Proc. Natl. Acad. Sci. USA (1995) 92:9029–9033CrossrefGoogle Scholar
  • Lau K. F., Dill K. A. A lattice statistical-mechanics model of the conformational and sequence-spaces of proteins. Macromolecules (1989) 22:3986–3997CrossrefGoogle Scholar
  • Leary R. H. Global optimization on funneling landscapes. J. Global Optim. (2000) 18:367–383CrossrefGoogle Scholar
  • Levy Y., Becker O. M. Effect of conformational constraints on the topography of complex potential energy surfaces. Phys. Rev. Lett. (1998) 81:1126–1129CrossrefGoogle Scholar
  • Levy Y., Jortner J., Becker O. M. Dynamics of hierarchical kinetics on the energy landscapes of hexapeptides. J. Chem. Phys. (2001) 115:10533–10547CrossrefGoogle Scholar
  • Li Z., Scheraga H. A. Monte-carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA (1987) 84:6611–6615CrossrefGoogle Scholar
  • Locatelli M., Schoen F. Fast global optimization of difficult Lennard-Jones clusters. Comput. Optim. Appl. (2002) 21:55–70CrossrefGoogle Scholar
  • Locatelli M., Schoen F. Efficient algorithms for large scale global optimization: Lennard-Jones clusters. Comput. Optim. Appl. (2003) 26:173–190CrossrefGoogle Scholar
  • Miller M. A., Wales D. J. Energy landscape of a model protein. J. Chem. Phys. (1999) 111:6610–6616CrossrefGoogle Scholar
  • Miller M. A., Doye J. P. K., Wales D. J. Structural relaxation in Morse clusters: Energy landscapes. J. Chem. Phys. (1999) 110:328–334CrossrefGoogle Scholar
  • Morè J. J., Wu Z., Di Pillo Giannessi. Smoothing techniques for macromolecular global optimization. Nonlinear Optimization and Applications (1996) (Plenum Press, New York) 297–312CrossrefGoogle Scholar
  • Morse P. M. Diatomic molecules according to the wave mechanics, II. Vibrational levels. Phys. Rev. (1929) 34:57–64CrossrefGoogle Scholar
  • Mortenson P. N., Wales D. J., Evans D. A. Energy landscapes of model polyalanines. J. Chem. Phys. (2002) 117:1363–1376CrossrefGoogle Scholar
  • Northby J. A. Structure and bonding of Lennard-Jones clusters: 13 ≤ n ≤ 147. J. Chem. Phys. (1987) 87:6166–6177CrossrefGoogle Scholar
  • Radford S. E., Dobson C. M., Evans P. A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature (1992) 358:302–307CrossrefGoogle Scholar
  • Roberts C., Johnston R. L., Wilson N. T. A genetic algorithm for the structural optimization of Morse clusters. Theoret. Chemistry Accounts (2000) 104:123–130CrossrefGoogle Scholar
  • Romero D., Barrón C., Gómez S. The optimal geometry of Lennard-Jones clusters: 148-309. Comp. Phys. Comm. (1999) 123:87–96CrossrefGoogle Scholar
  • The Cambridge Cluster Database (2004) . http://www-wales.ch.cam.ac.uk/CCD.htmlGoogle Scholar
  • Wales D. J., Doye J. P. K. Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A (1997) 101:5111–5116CrossrefGoogle Scholar
  • Wales D. J., Scheraga H. A. Global optimization of clusters, crystals and biomolecules. Science (1999) 285:1368–1372CrossrefGoogle Scholar
  • Wolf M. D., Landman U. Genetic algorithms for structural cluster optimization. J. Phys. Chem. A (1998) 102:6129–6137CrossrefGoogle Scholar
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