--------------------------------------------------------------- ANALYZE - Processing and Analysis of Peptide Confromation Data --------------------------------------------------------------- AUTHORS AND CONTRIBUTORS: ------------------------- Dr. Adam Liwo (adam@chemik.chem.univ.gda.pl) Dr. Cezary Czaplewski (czarek@scheraga2.chem.cornell.edu) Dr. Stanislaw Oldziej (stan@chemik.chem.univ.gda.pl) Dr. Malgorzata Groth Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18 80-952 Gdansk, Poland. Dr. Mark D. Shenderovich (marksh@strubix.com) Structural Bioinformatics, Inc. 10929 Technology Place San Diego, CA 92127 ------------------------------------------------------------------------------- 1. FUNCTIONS OF THE PROGRAM --------------------------- ANALYZE performs automatic processing and analysis of multiple conformation data of a polypeptide chain, including comparison of the results of theoretical calculations with the available experimental data (NMR spectra, coupling constants, inter-chromophore distances, etc.). In the current version ANALYZE processes the outo.* files (containing the dihedral angles phi, psi, omega, chi1,... chi_n, which define the geometry of polypeptide chains at all-atom level) obtained from global conformational analysis using ECEPPAK or generated otherwise. Specific functions of the program are as follows: 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. IMPORTANT! Another version of the NMR-fitting algorithm for processing the files generated with the AMBER package is also available. As the distribution version is in preparation, contact Adam Liwo (adam@chemik.chem.univ.gda.pl) or Cezary Czaplewski (czarek@scheraga2.chem.cornell.edu), if interested in obtaining the code. 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 5. Availability at TASK ----------------------- The package is installed in the /apl/chemia/analyze directory.