Elsevier Science Home
Computer Physics Communications Program Library
Full text online from Science Direct
Programs in Physics & Physical Chemistry
CPC Home

[Licence| Download | New Version Template] aabu_v1_0.gz(107 Kbytes)
Manuscript Title: Determination of proteinic structures: an experimentation program.
Authors: B. Coghlan, S. Fraga
Program title: POETA
Catalogue identifier: AABU_v1_0
Distribution format: gz
Journal reference: Comput. Phys. Commun. 36(1985)391
Programming language: Fortran.
Computer: AMDAHL 580/5860.
Operating system: MTS.
RAM: 600K words
Word size: 32
Peripherals: disc.
Keywords: Molecular physics, Structure, Proteins, Conformations, Optimization, Biology.
Classification: 3, 16.1.

Revision history:
Type Tit le Reference
adaptation 0001 AGAB See below

Nature of problem:
Determination of the spatial conformation of a protein from its amino acid sequence.

Solution method:
Optimization, under an energy criterion, by rotation around the bonds C alpha-C', C'-N, N-C alpha' and C alpha-C beta.

Restrictions:
Only proteins involving the amino acids ala, arg, asn, asp, cys, glu, gln, gly, his, ile, leu, met, phe, pro, ser, thr, trp, tyr, and val may be studied. The amino acid sequence of the protein must be known.

Unusual features:
The graphic representation of the protein may be obtained from the Cartesian coordinates of its atoms, produced by this program. The plotting subroutines, available at the institution where the program will be run, may be used for this purpose.

Running time:
Dependent on the size of the protein and the level of optimization. used.

ADAPTATION SUMMARY
Manuscript Title: Association of proteins: adaptation and coupling of two available programs.
Authors: L. Seijo, B. Coghlan, S. Fraga
Program title: 0001 AGAB
Catalogue identifier: AABU_v1_0
Distribution format: gz
Journal reference: Comput. Phys. Commun. 41(1986)169
Programming language: Fortran.
Computer: AMDHAL 580/5860.
Operating system: MTS.
Word size: 32
Classification: 3, 16.1.

Nature of problem:
Determination of the optimal spatial conformations and relative positions of two proteins from their amino acid sequence.

Solution method:
Optimization, under an energy criterion, by rotation around the bonds C alpha-C', C'-N, N-C alpha' and C alpha-C beta (see Fig 1).

Restrictions:
Only proteins involving the amino acids ala, arg, asn, asp, cys, glu, gln, gly, his, ile, leu, met, phe, pro, ser, thr, trp, tyr, and val may be studied. The amino acid sequence of the protein must be known.

Unusual features:
The graphic representation of the protein may be obtained from the Cartesian coordinates of its atoms, produced by this program. The plotting subroutines, available at the institution where the program will be run, may be used for this purpose.

Running time:
Dependent on the size of the protein and the level of optimization used.