V'asquez, M., N'emethy, G., and Scheraga, H. A. (1994). Conformational energy calculations on polypeptides and proteins. Chemical Reviews, 94:2183--2239. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
Deterministic Global Optimization For Protein Structure.. - Klepeis, Floudas (Correct)
....contributions are calculated and included at each minima of the upper and lower bounding functions. In this way, the progression of lower and upper bounds includes a temperature dependent entropic term. A similar modification to the Monte Carlo minimization method has also been proposed (V asquez et al. 1994), and has been shown to be effective in locating low energy conformers of peptides (Meirovitch and Meirovitch, 1997; Meirovitch and V asquez, 1997) The problem formulation is identical to the one given in (1.19) That is, the minimization of E and L are still performed using only potential and ....
V'asquez, M., N'emethy, G., and Scheraga, H. A. (1994). Conformational energy calculations on polypeptides and proteins. Chemical Reviews, 94:2183--2239.
Predicting Solvated Peptide Conformations via.. - Klepeis.. (1997) (Correct)
....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 class of nonlinear ....
V'asquez M., N'emethy G., and Scheraga H.A., 1994, Conformational energy calculations on polypeptides and proteins. Chemical Reviews 94, 2183--2239.
Protein Folding and Peptide Docking: A Molecular.. - Klepeis.. (1998) (1 citation) (Correct)
....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 ....
M. V'asquez, G. N'emethy and H. A. Scheraga, Conformational energy calculations on polypeptides and proteins, Chem. Rev., 94, (1994), 2183-2239.
Protein Folding: Computational Challenges - Pop (1996) (Correct)
.... that this is not the case and that the solvent affects protein electrostatics in a more complicated way [Har89] The entropy can be determined by examining the fluctuations of the structure around an energy minimum and computing the probability of the protein being in the particular minimum [VNS94] Several algorithms for the computation of entropy have been included in simulation programs like AMBER or CHARMM [WK81, BBO 83] 6 Disulfide bonds, hydrogen bonds, hydrophobicity Except for the interactions described in the previous section, several others affect the energy of proteins. ....
Maximiliano V'asquez, George N'emethy, and Harold A. Scheraga. Conformational energy calculations on polypeptides and proteins. Chemical Review, 94:2183--2239, 1994.
Global Optimization Approaches in Protein Folding and.. - Floudas, Klepeis.. (1999) (Correct)
....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 ....
M. V'asquez, G. N'emethy and H. A. Scheraga, Conformational energy calculations on polypeptides and proteins, Chem. Rev., 94, (1994), 2183-2239.
Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback
CiteSeer.IST - Copyright Penn State and NEC