P.M. Pardalos, D. Shalloway, and G. Xue. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, DIMACS Series Vol. 23. American Mathematical Society, 1996.  Home/Search   Document Not in Database   Summary   Related Articles   Check

.... [1] and performance guaranteed approximation algorithms have been developed for a variety of lattice models (e.g. see Hart and Istrail [6] A wide variety of global optimization techniques have been applied to PSP (e.g. see the papers in Biegler et al. 2] and Pardalos, Shalloway and Xue [9]) In particular, GAs have proven a particularly robust and e ective global optimization technique for PSP. For these methods, the embedding of a sequence in a lattice may be represented in a number of ways. Three common methods are Cartesian coordinates (the location of each acid on the lattice ....

P. M. Pardalos, D. Shalloway, and G. L. Xue, editors. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, volume 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, Providence, Rhode Island, 1996.

....When solvation energy is considered, as is the case in many MD and MC simulations, the search is strictly local. A number of recent review papers have surveyed the treatment of the protein conformation problem in terms of the global minimization of nonconvex energy functions (Neumaier, 1997; Pardalos et al. 1996; V asquez et al. 1994; Scheraga, 1992) This work addresses the protein folding problem, including the effects of solvation, through the use of a deterministic global optimization algorithm. This branch and bound based global optimization algorithm, known as ffBB, is applicable to a large ....

Pardalos P.M., Shalloway D., and Xue G. (eds.), 1996, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding , vol. 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Amer. Math. Soc.

....while others rely on simplifications of the potential model and or mathematical transformations. The major limitation is that there is no guarantee for convergence to the global minimum energy structure. A number of recent reviews have focused on global optimization issues for these systems [13, 28, 30, 33]. In this work, the global optimization approach ffBB has been extended to identifying global minimum energy conformations of solvated peptides and peptide docking complexes. The development of this branch and bound method was motivated by the need for an algorithm that could guarantee ....

P. M. Pardalos, D. Shalloway and G. Xue (editors) , Global minimization of nonconvex energy functions : Molecular conformation and protein folding, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23, Amer. Math. Soc., (1996).

.... [1] and performance guaranteed approximation algorithms have been developed for a variety of lattice models (e.g. see Hart and Istrail [6] A wide variety of global optimization techniques have been applied to PSP (e.g. see the papers in Biegler et al. 2] and Pardalos, Shalloway and Xue [9]) In particular, GAs have proven a particularly robust and effective global optimization technique for PSP. For these methods, the embedding of a sequence in a lattice may be represented in a number of ways. Three common methods are Cartesian coordinates (the location of each acid on the lattice ....

P. M. Pardalos, D. Shalloway, and G. L. Xue, editors. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, volume 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, Providence, Rhode Island, 1996.

....[268] and Pardalos et al. 229] survey, from different perspectives, the different methods for global optimization that have been used so far on molecular conformation problems. Together with the proceedings of the workshop on global minimization of nonconvex energy functions by Pardalos et al. [230], these give an up to date bibliography on this part of the literature. Online information on global optimization in general (including public domain software packages) can be found on the World Wide Web, e.g. at the address http: solon.cma.univie.ac.at neum glopt.html. Instead of describing ....

P. M. Pardalos, D. Shalloway and G. Xue, eds., Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Amer. Math. Soc., Providence, RI, 1996.

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P.M. Pardalos, D. Shalloway, and G. Xue. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, DIMACS Series Vol. 23. American Mathematical Society, 1996.

....the fundamental modeling issues for the protein folding and peptide docking problems, this review critically assesses a variety of global optimization approaches applied to these problems. A number of proceedings and reviews have also focused on global optimization issues in molecular systems [95, 132, 138, 139, 156, 177] GLOBAL OPTIMIZATION IN PROTEIN FOLDING AND PEPTIDE DOCKING 3 2. Energy Modeling 2.1. Potential Energy. In a rigorous sense, the dynamics of molecular motion are represented by Schrodinger s equation, which, when solved, yields an exact description of the energy as a function of structure. This ....

P. M. Pardalos, D. Shalloway and G. Xue (editors), Global minimization of nonconvex energy functions : Molecular conformation and protein folding, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23, Amer. Math. Soc., (1996).

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P. M. Pardalos, D. Shalloway, and G. L. Xue, editors. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding,volume23ofDIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1996.

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P. M. PARDALOS, D. SHALLOWAY, and G. XUE, editors. Global minimization of nonconvex energy functions: molecular conformation and protein folding, volume 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, Providence, RI, 1996.

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P. M. Pardalos, D. Shalloway, and G. Xue, editors, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, volume 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Amer. Math. Soc., 1996.

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