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286. ECEPP: Empirical Conformational Energy Programs
for Peptides
by M. J. Browman, L. M. Carruthers, K. L. Kashuba, F.
A. Momany, M. S. Pottle, S. P. Rosen, and S. M. Rumsey.
Write-up by G. F. Endres. Submitted by H. A. Scheraga,
Department of Chemistry, Cornell University, Ithaca,
New York 14853
This program computes the atomic coordinates and
relative conformational energy of a polypeptide chain
in standard geometry for any given sequence of residues
and set of dihedral angles. It is intended to be used
for the comparison of the relative energies of
different conformations of a given polypeptide and is
not valid for the comparison of the energies of
polypeptides with different sequences.
The empirical potential energy functions, energy
parameters, and geometric parameters used in this
program are described in the literature. The program
treats linear polypeptides and those containing one or
more intramolecular disulfide linkages (cystine
residues), but not polypeptides with cyclic peptide
backbones. It reads as initial input a data set
containing standard residue information to be used in
the subsequent generation of atomic coordinates and
computation of relative potential energy. The Standard
Residue Data supplied with the program (Section II C)
consists of a basic data set for 26 amino acid residues
commonly found in proteins and many end groups present
in synthetic polypeptides. If any residues or end
groups are not needed in a particular application, an
abbreviated set can be used. Any properly formatted
residue can be substituted for the supplied data, e.g.,
if the user does not wish to use the supplied standard
geometry.
The user supplies additional data cards specifying:
1. the number of conformations to be treated,
the desired amino acid sequence, including end
groups, and the designation of the
stereochemistry (D or L) of each amino acid
residue
2. the pairing of half-cystine residues in
intramolecular disulfide bonds
3. the initial conformation (by supplying values
of all dihedral angles)
4. which dihedral angles will be treated as
variables, i.e., which will differ in subsequent
conformations
5. new values of these variables for each
subsequent conformation
The program calls a set of subroutines to generate the
atomic coordinates for each conformation (Section II
A), using bond lengths and bond angles defined in the
standard data set and the dihedral angles specified by
the user. Another set of subroutines is called to
compute the total conformational energy (ETOT), using
empirical potential energy functions (Section II B).
ETOT is computed as the sum of these component
energies: electrostatic (EES); nonbonded plus hydrogen
bonded (ENB); general torsional (ETOR); cystine bridge
torsional (ECYSTR); and a loop-closing potential for S-
S bonds (ELOOP). As described in Section II B, the
repulsive part of the nonbonded interaction energy is
reduced by a factor of 0.5 if a particular interaction
is "1-4", i.e., between a pair of atoms separated by
only one bond whose rotation affects their interatomic
distance. A group of subroutines is used to specify
which interactions are 1-4 type for a given polypeptide
sequence (Section II D).
The output of the program includes the atomic
coordinates, the total conformational energy and its
five components, for each conformation. The sample
main program included here can be modified to carry out
grid searches, compute conformational energy maps (d-c
plots), or (in combination with a function-minimizing
subroutine) find conformations corresponding to local
energy minima.
FORTRAN IV (IBM 360/370)
Lines of Code: 4303
Recommended Citation: M. J. Browman et al., QCPE 11,
286 (1975).
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