N'emethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A. (1992). Energy parameters in polypeptides. 10. J. Phys. Chem., 96:6472--6484. Home/Search Document Not in Database Summary Related Articles Check |
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Deterministic Global Optimization For Protein Structure.. - Klepeis, Floudas (Correct)
....form of individual energy terms based on the phenomenological nature of that term. Other simplified models have been used to reduce the degrees of freedom associated with the conformational energy expressions. For this work the ECEPP 3 (Empirical Conformational Energy Program for Peptides) N emethy et al. 1992) potential model is utilized. In this force field, it is assumed that the covalent bond lengths and bond angles are fixed at their equilibrium values. Then, the conformation is only a function of the independent torsional angles of the system, also known as dihedral angles. The total ....
....are computed as the sum of terms for each atom pair (i,j) whose interatomic distance is a function of at least one dihedral angle. The general potential energy terms of ECEPP 3 are shown in Figure 1. 2, while the development of the appropriate parameters is discussed and reported elsewhere (N emethy et al. 1992). 3.2 SOLVATION ENERGY MODELS Solvation contributions are generally believed to be a significant force in stabilizing the native conformations of proteins. Explicit methods can be used to include solvation effects by actually surrounding the polypeptide with solvent molecules and calculating ....
[Article contains additional citation context not shown here]
N'emethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A. (1992). Energy parameters in polypeptides. 10. J. Phys. Chem., 96:6472--6484.
Predicting Solvated Peptide Conformations via.. - Klepeis.. (1997) (Correct)
.... of molecular potential functions include ECEPP (Momany et al. 1975, 1974a,b) AMBER (Weiner et al. 1986, 1984) CHARMM (Brooks et al. 1983) DISCOVER (Dauber Osguthorpe et al. 1988) GROMOS (van Groningen and Berendsen, 1987) MM3 (Allinger et al. 1989) ENCAD (Levitt, 1983) ECEPP 2 (N emethy et al. 1983) and ECEPP 3 (N emethy et al. 1992) In general, these models, also known as force fields, are expressed as summations of empirically derived potential functions, with the mathematical form of individual energy terms based on the phenomenological nature of that term. Constants describing ....
N'emethy G., Pottle M.S., and Scheraga H.A., 1983, Energy parameters in polypeptides. 9.
Predicting Solvated Peptide Conformations via.. - Klepeis.. (1997) (Correct)
.... include ECEPP (Momany et al. 1975, 1974a,b) AMBER (Weiner et al. 1986, 1984) CHARMM (Brooks et al. 1983) DISCOVER (Dauber Osguthorpe et al. 1988) GROMOS (van Groningen and Berendsen, 1987) MM3 (Allinger et al. 1989) ENCAD (Levitt, 1983) ECEPP 2 (N emethy et al. 1983) and ECEPP 3 (N emethy et al. 1992). In general, these models, also known as force fields, are expressed as summations of empirically derived potential functions, with the mathematical form of individual energy terms based on the phenomenological nature of that term. Constants describing molecular geometry, such as bond lengths and ....
....as the sum of the electrostatic, nonbonded, hydrogen bonded, and torsional contributions. There is also a pseudo potential for loop closing if the polypeptide contains two or more sulfur containing residues. More recent work by includes a revised treatment of prolyl and hydroxyprolyl residues (N emethy et al. 1992). For each prolyl or hydroxyprolyl residue contained in the polypeptide a fixed internal conformational energy for the pyrolidine ring is added. The main energy contributions (electrostatic, nonbonded, hydrogen bonded) are computed as the sum of terms for each atom pair (i,j) whose interatomic ....
[Article contains additional citation context not shown here]
N'emethy G., Gibson K.D., Palmer K.A., Yoon C.N., Paterlini G., Zagari A., Rumsey S., and Scheraga H.A., 1992, Energy parameters in polypeptides. 10. J. Phys. Chem. 96, 6472--6484.
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