Global Optimization of Morse Clusters by Potential Energy Transformations
Published Online:1 Nov 2004https://doi.org/10.1287/ijoc.1040.0084
References
- Free energy landscape for protein folding kinetics: Intermediates, traps and multiple pathways in theory and lattice model simulations. J. Chem. Phys. (1994) 101:6052–6062Crossref, Google Scholar
- 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
- Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins (1995) 21:167–195Crossref, Google Scholar
- The effect of compression on the global optimization of atomic clusters. Phys. Rev. E (2000) 62:8753–8761Crossref, Google Scholar
- Structural consequences of the range of the interatomic potential: A menagerie of clusters. J. Chem. Soc. Faraday Trans. (1997) 93:4233–4244Crossref, Google Scholar
- Thermodynamics of global optimization. Phys. Rev. Lett. (1998) 80:1357–1360Crossref, Google Scholar
- Evolution of the potential energy surface with size for Lennard-Jones clusters. J. Chem. Phys. (1999) 111(18):8417–8428Crossref, Google Scholar
- Global optimization and the energy landscapes of Dzugutov clusters. Faraday Discuss (2001a) 118:159–170Crossref, Google Scholar
- Modelling the structure of C60 clusters. Phys. Rev. B (2001b) 64:1–11Crossref, Google Scholar
- Kinetics of protein-folding—Nucleation mechanism, time scales, and pathways. Biopolymers (1995) 36:83–102Crossref, Google Scholar
- Kinetic traps in lysozyme folding. Proc. Natl. Acad. Sci. USA (1995) 92:9029–9033Crossref, Google Scholar
- A lattice statistical-mechanics model of the conformational and sequence-spaces of proteins. Macromolecules (1989) 22:3986–3997Crossref, Google Scholar
- Global optimization on funneling landscapes. J. Global Optim. (2000) 18:367–383Crossref, Google Scholar
- Effect of conformational constraints on the topography of complex potential energy surfaces. Phys. Rev. Lett. (1998) 81:1126–1129Crossref, Google Scholar
- Dynamics of hierarchical kinetics on the energy landscapes of hexapeptides. J. Chem. Phys. (2001) 115:10533–10547Crossref, Google Scholar
- Monte-carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA (1987) 84:6611–6615Crossref, Google Scholar
- Fast global optimization of difficult Lennard-Jones clusters. Comput. Optim. Appl. (2002) 21:55–70Crossref, Google Scholar
- Efficient algorithms for large scale global optimization: Lennard-Jones clusters. Comput. Optim. Appl. (2003) 26:173–190Crossref, Google Scholar
- Energy landscape of a model protein. J. Chem. Phys. (1999) 111:6610–6616Crossref, Google Scholar
- Structural relaxation in Morse clusters: Energy landscapes. J. Chem. Phys. (1999) 110:328–334Crossref, Google Scholar
- , Di Pillo Giannessi. Smoothing techniques for macromolecular global optimization. Nonlinear Optimization and Applications (1996) (Plenum Press, New York) 297–312Crossref, Google Scholar
- Diatomic molecules according to the wave mechanics, II. Vibrational levels. Phys. Rev. (1929) 34:57–64Crossref, Google Scholar
- Energy landscapes of model polyalanines. J. Chem. Phys. (2002) 117:1363–1376Crossref, Google Scholar
- Structure and bonding of Lennard-Jones clusters: 13 ≤ n ≤ 147. J. Chem. Phys. (1987) 87:6166–6177Crossref, Google Scholar
- The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature (1992) 358:302–307Crossref, Google Scholar
- A genetic algorithm for the structural optimization of Morse clusters. Theoret. Chemistry Accounts (2000) 104:123–130Crossref, Google Scholar
- The optimal geometry of Lennard-Jones clusters: 148-309. Comp. Phys. Comm. (1999) 123:87–96Crossref, Google Scholar
- The Cambridge Cluster Database (2004) . http://www-wales.ch.cam.ac.uk/CCD.htmlGoogle Scholar
- Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A (1997) 101:5111–5116Crossref, Google Scholar
- Global optimization of clusters, crystals and biomolecules. Science (1999) 285:1368–1372Crossref, Google Scholar
- Genetic algorithms for structural cluster optimization. J. Phys. Chem. A (1998) 102:6129–6137Crossref, Google Scholar

