+++ /dev/null
-* This software is provided free of charge to academic users, subject to the
- condition that no part of it be sold or used otherwise for commercial
- purposes, including, but not limited to its incorporation into commercial
- software packages, without written consent from the authors. For permission
- contact Prof. H. A. Scheraga, Cornell University.
-
-* This software package is provided on an "as is" basis. We in no way warrant
- either this software or results it may produce.
-
-* Reports or publications using this software package must contain an
- acknowledgement to the authors and the NIH Resource in the form commonly used
- in academic research.
-
- DESCRIPTION OF UNRES/CSA EXAMPLES
-
-
-1. General notes
-----------------
-
-The input and output files pertaining to the variations of the UNRES force field
-described in UNRES.TXT are in the directory examples and subdirectories CASP3, ALPHA,
-BETA, ALPHABETA, CASP5, 3P, and 4P, respectively. Each of these directories
-contains subdirectory ENERGY and CSA; these contain examples of single-point
-energy evaluation and minimization and CSA search, respectively. Both ENERGY
-and CSA directories contain output subdirectories with sample output files; input
-and script files are on the root level. Additionally, CASP5/CSA and ALPHABETA/CSA are
-further divided into subdirectories pertaining to specific systems.
-
-The examples contained in ENERGY must be run to test a variation of the force field.
-Check the energies obtained in output/*.out_GB000 (BEFORE minimzation) with your
-results. Differences in any component larger than the last significant digit mean
-that there is an error in your settings or installation. (Note that the differences
-in energies AFTER minimization might be greater and are not a reason to worry.)
-Check carefully the parameter files, in the C-shell script, the energy-term weights
-in the *.inp file and the compiler flags specified in section 4. of UNRES.TXT. If
-the differences persist, report the problem to the authors (contact information is
-at the end of this file and UNRES.TXT. The energies (before and after minimization)
-are listed in the title lines of the input files.
-
-The CSA results are stochastic and you might happen to get completely different
-results than those contained in the output directories. Apart from (perhaps)
-ALPHA and 4P the other force fields exhibit some "glassy" behavior with the CSA
-search method and the search happens to be trapped in higher-energy regions.
-For each example, we have provided the lowest energy reached so far for that system,
-if different from that in the example. We also provided the respective native
-structure.
-
-To save space, in all cases except CASP5 only the master output file is provided.
-See section 3. of UNRES.TXT for the description of the output files.
-
-The C-shell scripts for single-point energy evaluation are for interactive runs,
-while those for CSA calculations are for batch runs. In each case the master batch
-script is start.mat. The batch scripts are for the PBS system.
-
-2. Single-point energy evaluation and minimization tests
---------------------------------------------------------
-
-CASP3
-
-The input file protA.inp and the pertinent output files in output contain the data
-and results of energy evaluation and subsequent minimization of the NMR structure
-of the 46-residue fragment of the B-domain of staphylococcal protein A. The
-C-shell script file is unres_casp3.csh.
-
-The input file proteinA_rms.inp and the pertinent output files contain the data and
-results of energy evaluation and minimization and the evaluation of the RMSD from the
-NMR structure (prota_nmr.pdb) for a native-like conformation obtained in CSA
-search; this structure is native-like [1].
-
-ALPHA
-
-The input file T0102.inp and the pertinent output files contain the data and results
-of energy evaluation and minimization of the lowest-energy structure of bacteriocin
-As-48 (CASP4 target T0102; PDB code: 1E68) obtained in the CASP4 exercise [2]. The
-structure is native-like.
-
-BETA
-
-The input file T0105.inp and the pertinent output files contain the data and results
-of energy evaluation and minimization of the lowest-energy structure of the human
-Sp100B sand domain (CASP4 target T0105; PDB code: 1H5P). This middle beta-hairpin
-corresponds to the hairpin in the native structure.
-
-ALPHABETA
-
-The input file T0104.inp and the pertinent output files contain the data and results
-of energy evaluation and minimization of the lowest-energy conformation of Yjee
-protein (CASP4 target T0104; PDB code: 1FL9). The structure has some similarity to
-the native structure in the N-terminal part.
-
-CASP5
-
-The input file 1igd.inp and the pertinent output files contain the data and results
-of energy calculation and minimization for for the lowest-energy structure of the
-IGG domain (1IGD). The structure is native-like except misalignment of the two
-beta-hairpins. The C-shell script is unres_casp5_1igd.csh.
-
-The input file t0132.inp and the pertinent output files contain the data and results
-of energy calculation and minimization for the lowest-energy conformation of
-HI0827 (CASP5 target: T0132). The structure shares some features with the native
-structures; the latter has not been published yet. The C-shell script is
-unres_casp5_t0149c.csh.
-
-The input file T0149C_dihc.inp and the pertinent output files contain the data and
-results of energy calculation and minimization for the lowest-energy conformation of
-the C-terminal domain of the Yjia protein (CASP5 target: T0149; PDB code: 1NIJ).
-The structure shares and about 80-residue segment with the native structure.
-The C-shell script is unres_casp5_t0149c.csh. Dihedral-angle restraints from
-secondary-structure prediction were used; they are included in T0149C_dihc.spred.
-
-3P
-
-The file IGD_3P7_iter81_1_i1.inp and the pertinent output files contain the results
-of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD.
-The structure shares the topology with the native structure, but the RMSD is
-6.3 A.
-
-4P
-
-The file 4P5_iter33_3_i3.inp and the pertinent output files contain the results
-of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD.
-The structure shares the topology with the native structure, but the RMSD is about
-5.6 A.
-
-3. CSA calculations
--------------------
-
-CASP3
-
-The example pertains to protein A. The search resulted in the mirror image of
-the native structure (which is not the lowest-energy structure; the lowest energy
-ever found is -157.103 kcal/mol and corresponds to a native-like structure).
-Native-like structures are, however, present in the final bank. The files
-proteinA_CASP3@???.pdb contain the lowest-energy conformations found by CSA every
-100 minimizations; they can be used to construct the "evolution path" of the
-system. The experimental structure is in prota_nmr.pdb.
-
-ALPHA
-
-The example also pertains to protein A. The search results in a native-like
-structure as the lowest-energy structure with RMSD=3.2 A from the NMR structure.
-The experimental structure is in prota_nmr.pdb.
-
-BETA
-
-The example pertains to the betanova three-stranded beta-sheet peptide. The native-
-like structure is obtained in the search. The experimental structure is in
-bh35.pdb (it should be noted that this structure was not accepted by the PDB and
-the only certain information from the experiment is that this peptide forms
-predominantly a three-stranded beta-sheet).
-
-ALPHABETA
-
-The CSA directory is divided into the BETANOVA and proteinA subdirectories for
-these two molecules. In both cases the search results in a native-like structure
-as the lowest-energy structure.
-
-CASP5
-
-The example pertains to the 1FSD alpha/beta peptide. The directory run1 corresponds
-to a "successful" run in which a native-like alpha/beta structure was obtained, while
-the directory run2 to an "unsuccesful" one, in which a three-stranded non-native
-beta-sheet was obtained as the lowest-energy structure. However, even this
-native-like structure has a higher energy than the lowest energy structure found
-so far (-77.518 kcal/mol; native-like). The NMR structure is in 1FSD.pdb.
-
-3P
-
-The example pertains to 1IGD. This run has led to a non-native "negative" of
-the protein, in which the beta-sheet is formed in the middle of the sequence and
-not in the N- and the C-end. The energy is much higher than that of the lowest-energy
-native structure, which is -745.355 kcal/mol. The native structure is in 1igd.pdb.
-
-4P
-
-Another 1IGD example; this time the search resulted in the native structure.
-However, the energy is higher than the lowest energy found (-747.433 kcal/mol).
-
-
-4. References
--------------
-
-[1] J. Lee, A. Liwo, H.A. Scheraga. Conformational space annealing and an
- off-lattice united-residue force field: application to the 10-55 fragment of
- staphylococcal protein A and to apo calbindin D9K. Proc. Natl. Acad. Sci. USA},
- 1999, 96, 2025-2030.
-
-[2] J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D.R. Ripoll, R. Kazmierkiewicz,
- St. Oldziej, W.J. Wedemeyer, K.D. Gibson, Y.A. Arnautova, J. Saunders,
- Y.-J. Ye, H. A. Scheraga. Recent improvements in prediction of protein structure
- by global optimization of a potential energy function. Proc. Natl. Acad. Sci.
- USA, 2001, 98, 2329--2333.
-
-
-
-5. Contact information
-----------------------
-
- Dr. Adam Liwo
- Faculty of Chemistry, University of Gdansk
- ul. Sobieskiego 18, 80-952 Gdansk Poland.
- phone: +48 58 345 0361
- fax: +48 58 341 0357
- e-mail: adam@chem.univ.gda.pl
-
- Dr. Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk
- ul. Sobieskiego 18, 80-952 Gdansk Poland.
- phone: +48 58 345 0361
- fax: +48 58 341 0357
- e-mail: czarek@chem.univ.gda.pl
-
- Dr. Stanislaw Oldziej
- Baker Laboratory of Chemistry and Chemical Biology
- Cornell University
- Ithaca, NY 14853-1301, U.S.A.
- phone: (607) 255 0556
- fax: (607) 255 4137
- e-mail: stan@scheraga2.chem.cornell.edu
-
- Dr. Jaroslaw Pillardy
- Baker Laboratory of Chemistry and Chemical Biology
- Cornell University
- Ithaca, NY 14853-1301, U.S.A.
- phone: (607) 255 0556
- fax: (607) 255 4137
- e-mail: jp86@cornell.edu
-
- Dr. Jooyoung Lee
- Korea Institute for Advanced Study
- 207-43 Cheongryangri-dong Dongdaemun-gu
- Seoul 130-012, Korea
- phone: 82-2-958-3731
- fax: 82-2-958-3786
- e-mail: jlee@kias.re.kr
-
-Prepared by Adam Liwo, Cezary Czaplewski, and Stanislaw Oldziej, 9/1/03
projects / unres.git / blobdiff