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	          PROTARCH
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A system of computer programs for hierarchical prediction
of protein structure based on the thermodynamic hypothesis.
The key stage of the method is global optimization of the
energy of a polypeptide chain at the simplified
united-residue level. This task is carried out with the use
of the UNRES force field and the Conformational Space
Annealing (CSA) method. PROTARCH includes also
computational tools to carry out cluster analysis and
construction of all-atom backbone from the united-residue
chain using the dipole-path method. 


AUTHORS AND CONTRIBUTORS: 

         1,2            1                  1                 3                 1
Adam Liwo,  Jooyoung Lee, Jaroslaw Pillardy, Daniel R. Ripoll, Ryszard J. Wawak,
                 1,2                      2                  2                 2
 Cezary Czaplewski, Rajmund Kazmierkiewicz, Stanislaw Oldziej, Malgorzata Groth,
                                      4                 5
                     Matthew R. Pincus, Shelly Rackovsky,
                                               1
                             Harold A. Scheraga

1
 Baker Laboratory of Chemistry and Chemical Biology, Cornell University,
 Ithaca, NY 14853-1301, U.S.A.
2
 Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18,
 80-952 Gdansk, Poland
3
 Cornell Cornell Theory Center, Cornell University,
 Ithaca, NY 14853-3801, U.S.A.
4
 Department of Pathology, Brooklyn Veterans Administration Medical Center,
 Brooklyn, N.Y. 11209
5
 Department of Biomathematical Sciences, Mount Sinai School of Medicine,
 One Gustave L. Levy Place, New York, N.Y. 10029, U.S.A.

Note:
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This is a preliminary release of the PROTARCH package for protein structure
prediction based on the thermodynamic hypothesis. The key stage of the
method is global optimization of the energy of a polypeptide chain at the
simplified united-residue level. This task is carried out with the use
of the UNRES force field and the Conformational Space Annealing (CSA)
method. The united-residue force field is now good for helical conformations,
but produces too distorted beta-sheet structures. Work to surmount the
beta-sheet problem is in progress.