1. FUNCTIONS OF THE PROGRAM
---------------------------
ANALYZE processes the dihehral-angle outo.* files obtained from 
calculations (usually global conformational analysis with the EDMC
method) using ECEPPAK. These functions include the following:

1. Calculations of conformational characteristics, such as hydrogen bonds,
   turn position and types, RMS deviation from a reference conformation,
   interchromophore distances, interproton distances, etc.

2. Calculation of Boltzmann-averaged properties of the conformational 
   ensemble.

3. Calculate the dihedral angles from supplied Cartesian coordinates.

4. Cluster analysis of the conformational ensemble by the minimal spanning
   tree or minimum-variance method.

5. Fitting the statistical weights of the conformations so as to achieve
   the best agreement between the calculated average and experimental NOE
   spectra and coupling constants. 

Details of the functions can be found in INPUT.DOC

2. CONTENTS 
-----------
The package includes two versions of ANALYZE: one for fitting NMR spectra
and one for cluster analysis and other purposes. The source files are 
contained in source_clust and source_nmr, respectively. This division is 
caused by practical reasons: the NMR and clustering parts are very memory 
consuming, which practically excludes their incorporation into one program. 

This NMR part of ANALYZE includes the core part of the MORASS package from 
Dr. D. Gorenstein laboratory, Sealy Center for Structural Biology, 
University of Texas Medical Branch, Galveston, TX (http://www.nmr.utmb.edu/).

The authors of ANALYZE are grateful to the MORASS developer group for the 
permission of including the MORASS modules in the publicly available version 
of ANALYZE. Note that this permission was granted subject to the condition 
that the software remains free for academic and educational use,
as is the MORASS package.

For more information about MORASS see http://www.nmr.utmb.edu/#mrass.

For the program to work, some database files are required. The location
of the database directory must be specified by the DBASDIR environmental
variable. See INSTALL.DOC and COMMAND.DOC for details.

3. AVAILABILITY AND CITING
--------------------------
The package is available for free to academic users. When publishing the 
work based on this program please cite the following references:

ECEPP/ECEPPAK:

1. F.A. Momany, R.F. McGuire, A.W. Burgess and H.A. Scheraga,
   J. Phys. Chem., 79, 2361-2381 (1975).

2. G. Nemethy and H.A. Scheraga, J. Phys. Chem. 87, 1883-1891 (1983).

3. M.J. Sippl, G. Nemethy, and H.A. Scheraga, J. Phys. Chem. 88, 6231-6233 
   (1984).

4. G. Nemethy, K.D. Gibson, K.A. Palmer, C.N. Yoon, C.N., G. Paterlini, 
   A. Zagari, S. Rumsey, S., and H.A. Scheraga, H.A. J. Phys. Chem., 96, 
   6472-6484 (1992).

5. D.R. Ripoll, M.S. Pottle, K.D. Gibson, A. Liwo and H.A. Scheraga.
   J. Comput. Chem., 16, 1153-1163 (1995).

6. D.R. Ripoll, A. Liwo and C. Czaplewski. TASK Quart., 3, 313-323 (1999).

NMR fitting:

1. J. Malicka, M. Groth, C. Czaplewski, A. Liwo, W. Wiczk, and L. Lankiewicz.
   Lett. Pept. Sci., 5, 445-447 (1998).

2. M. Groth, J. Malicka, C.  Czaplewski, S. Oldziej, L. Lankiewicz, 
   W. Wiczk and A. Liwo, J. Biomol. NMR, 4, 315-330 (1999).

3. D.R. Ripoll, A. Liwo and C. Czaplewski. TASK Quart., 3, 313-323 (1999).

MORASS:

1. Robert P. Meadows, Carol Beth Post, Bruce A. Luxon, and David G. Gorenstein,
   MORASS 2.1, Purdue University, W. Lafayette (1994).

2. C.B. Post, R.P. Meadows and D.G. Gorenstein, J. Am. Chem. Soc., 112, 6796 
   (1990)

4. SUPPORT 
----------
User's feedback is greatly appreciated. Please send questions and comments
to:

Dr. Adam Liwo
Faculty of Chemistry, University of Gdansk
Sobieskiego 18, 80-952 Gdansk, Poland

e-mail: adam@rutyl.chem.univ.gda.pl

or

Dr. Cezary Czaplewski
Baker Laboratory of Chemistry, Cornell University
Ithaca, NY 14853-1301

e-mail: czarek@scheraga2.chem.cornell.edu