ECEPP

The Empirical Conformational Energy Program for Peptides, ECEPP [63, 64], is one of the first empirical interatomic potentials whose derivation is based both on gas-phase and X-ray crystal data [65], It was developed in 1975 and updated in 1983 and 1992. The actual distribution (dated May, 2000) can be downloaded without charge for academic use. 

D.R. Ripoll, H.A. Scheraga, ECEPP Empirical Conformational Energy Program for Peptides, in The Encyclopedia of Computational Chemistry, Vol. 2,... 

Empirical conformational energy program for peptides (ECEPP) is the name of both a computer program and the force field implemented in that program. This is one of the earlier peptide force fields that has seen less use with the introduction of improved methods. It uses three valence terms that are fixed, a van der Waals term, and an electrostatic term. 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

IK Roterman, MH Lambert, KD Gibson, HA Scheraga. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. PHI-PSI maps for N-acetyl alanine N -methyl amide Comparisons, contrasts and simple experimental tests. J Biomol Stiaict Dyn 7 421-453, 198. 

G Nemethy, KD Gibson, KA Palmer, CN Yoon, G Paterlini, A Zagari, S Rumsey, FIA Scher-aga. Energy parameters in peptides. Improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to prolme-contammg peptides. J Phys Chem 96 6472-6484, 1992. 

ECEPP fixed fixed fixed 6-12 10-12 charge none proteins... 

Figure 5. Potential energy as a function of time for the octa-peptide simulation at 300K starting from (a) an a-helix, and (b) from a structure provided by ECEPP.

ECEPP Empirical conformational energy program for peptides... 

Some of the parameters that are used in the computer program ecepp (empirical conformational energy program for peptides) of Momany et al. (J. Phys. Chem. 1975, 79, 2361) are updated. The changes are based on experimental information that has become available since 1975,... 

N 103 "A Comparison of the CHARMM, AMBER, and ECEPP Potentials for Peptides. II Acetyl Alanine IV-Methyl Amide ... 

Some of the more approximate or specialized FFs encountered in the literature include CFF, CHEM-X, COSMIC, CYFF, DREIDING, MMX, SHAPES, TRIPOS, VALBOND, and UFF. Well-known FFs for modeling proteins and nucleic acids include AMBER, CHARMM, ECEPP, GROMOS, OPLS and their variants. Some of these latter FFs compromise the quality of reproducing subtle intramolecular electronic effects for the sake of being fast enough to treat biomacromolecules in long molecular simulations. 

Roterman IK, Gibson KD, Scheraga HA (1989) A comparison of the CHARMM, AMBER, and ECEPP/2 potential for peptides I, J Biomol Struct Dynamics, 7 391-419... 

Several algorithmic formulations have been developed for computations on peptides and proteins. Those in most widespread use are AMBER,46-47 CHARMM,48 DISCOVER,49 and ECEPP.23-50"52 Similar formulations are... 

Quantitatively, these functions (e.g., in ECEPP) are given by the expression... 

The quantity U , i , x is computed by summing over the ECEPP energies of all pairs of nonbonded atoms of the whole molecule. Equations [11] and [12] are used to compute conditional free energy (4>,i]i) contour maps, similar to standard conformational energy (< >, ) contour maps, for each residue of the polypeptide. The probable conformation of the /th residue is taken as the one of lowest conditional free energy, and the probable conformation of the whole polypeptide chain is assumed to be the combination of the probable conformations of the individual residues. 

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