1 * This software is provided free of charge to academic users, subject to the
2 condition that no part of it be sold or used otherwise for commercial
3 purposes, including, but not limited to its incorporation into commercial
4 software packages, without written consent from the authors. For permission
5 contact Prof. H. A. Scheraga, Cornell University.
7 * This software package is provided on an "as is" basis. We in no way warrant
8 either this software or results it may produce.
10 * Reports or publications using this software package must contain an
11 acknowledgement to the authors and the NIH Resource in the form commonly used
14 DESCRIPTION OF UNRES/CSA EXAMPLES
20 The input and output files pertaining to the variations of the UNRES force field
21 described in UNRES.TXT are in the directory examples and subdirectories CASP3, ALPHA,
22 BETA, ALPHABETA, CASP5, 3P, and 4P, respectively. Each of these directories
23 contains subdirectory ENERGY and CSA; these contain examples of single-point
24 energy evaluation and minimization and CSA search, respectively. Both ENERGY
25 and CSA directories contain output subdirectories with sample output files; input
26 and script files are on the root level. Additionally, CASP5/CSA and ALPHABETA/CSA are
27 further divided into subdirectories pertaining to specific systems.
29 The examples contained in ENERGY must be run to test a variation of the force field.
30 Check the energies obtained in output/*.out_GB000 (BEFORE minimzation) with your
31 results. Differences in any component larger than the last significant digit mean
32 that there is an error in your settings or installation. (Note that the differences
33 in energies AFTER minimization might be greater and are not a reason to worry.)
34 Check carefully the parameter files, in the C-shell script, the energy-term weights
35 in the *.inp file and the compiler flags specified in section 4. of UNRES.TXT. If
36 the differences persist, report the problem to the authors (contact information is
37 at the end of this file and UNRES.TXT. The energies (before and after minimization)
38 are listed in the title lines of the input files.
40 The CSA results are stochastic and you might happen to get completely different
41 results than those contained in the output directories. Apart from (perhaps)
42 ALPHA and 4P the other force fields exhibit some "glassy" behavior with the CSA
43 search method and the search happens to be trapped in higher-energy regions.
44 For each example, we have provided the lowest energy reached so far for that system,
45 if different from that in the example. We also provided the respective native
48 To save space, in all cases except CASP5 only the master output file is provided.
49 See section 3. of UNRES.TXT for the description of the output files.
51 The C-shell scripts for single-point energy evaluation are for interactive runs,
52 while those for CSA calculations are for batch runs. In each case the master batch
53 script is start.mat. The batch scripts are for the PBS system.
55 2. Single-point energy evaluation and minimization tests
56 --------------------------------------------------------
60 The input file protA.inp and the pertinent output files in output contain the data
61 and results of energy evaluation and subsequent minimization of the NMR structure
62 of the 46-residue fragment of the B-domain of staphylococcal protein A. The
63 C-shell script file is unres_casp3.csh.
65 The input file proteinA_rms.inp and the pertinent output files contain the data and
66 results of energy evaluation and minimization and the evaluation of the RMSD from the
67 NMR structure (prota_nmr.pdb) for a native-like conformation obtained in CSA
68 search; this structure is native-like [1].
72 The input file T0102.inp and the pertinent output files contain the data and results
73 of energy evaluation and minimization of the lowest-energy structure of bacteriocin
74 As-48 (CASP4 target T0102; PDB code: 1E68) obtained in the CASP4 exercise [2]. The
75 structure is native-like.
79 The input file T0105.inp and the pertinent output files contain the data and results
80 of energy evaluation and minimization of the lowest-energy structure of the human
81 Sp100B sand domain (CASP4 target T0105; PDB code: 1H5P). This middle beta-hairpin
82 corresponds to the hairpin in the native structure.
86 The input file T0104.inp and the pertinent output files contain the data and results
87 of energy evaluation and minimization of the lowest-energy conformation of Yjee
88 protein (CASP4 target T0104; PDB code: 1FL9). The structure has some similarity to
89 the native structure in the N-terminal part.
93 The input file 1igd.inp and the pertinent output files contain the data and results
94 of energy calculation and minimization for for the lowest-energy structure of the
95 IGG domain (1IGD). The structure is native-like except misalignment of the two
96 beta-hairpins. The C-shell script is unres_casp5_1igd.csh.
98 The input file t0132.inp and the pertinent output files contain the data and results
99 of energy calculation and minimization for the lowest-energy conformation of
100 HI0827 (CASP5 target: T0132). The structure shares some features with the native
101 structures; the latter has not been published yet. The C-shell script is
102 unres_casp5_t0149c.csh.
104 The input file T0149C_dihc.inp and the pertinent output files contain the data and
105 results of energy calculation and minimization for the lowest-energy conformation of
106 the C-terminal domain of the Yjia protein (CASP5 target: T0149; PDB code: 1NIJ).
107 The structure shares and about 80-residue segment with the native structure.
108 The C-shell script is unres_casp5_t0149c.csh. Dihedral-angle restraints from
109 secondary-structure prediction were used; they are included in T0149C_dihc.spred.
113 The file IGD_3P7_iter81_1_i1.inp and the pertinent output files contain the results
114 of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD.
115 The structure shares the topology with the native structure, but the RMSD is
120 The file 4P5_iter33_3_i3.inp and the pertinent output files contain the results
121 of energy evaluation and minimization of the lowest-enerrgy conformation of 1IGD.
122 The structure shares the topology with the native structure, but the RMSD is about
130 The example pertains to protein A. The search resulted in the mirror image of
131 the native structure (which is not the lowest-energy structure; the lowest energy
132 ever found is -157.103 kcal/mol and corresponds to a native-like structure).
133 Native-like structures are, however, present in the final bank. The files
134 proteinA_CASP3@???.pdb contain the lowest-energy conformations found by CSA every
135 100 minimizations; they can be used to construct the "evolution path" of the
136 system. The experimental structure is in prota_nmr.pdb.
140 The example also pertains to protein A. The search results in a native-like
141 structure as the lowest-energy structure with RMSD=3.2 A from the NMR structure.
142 The experimental structure is in prota_nmr.pdb.
146 The example pertains to the betanova three-stranded beta-sheet peptide. The native-
147 like structure is obtained in the search. The experimental structure is in
148 bh35.pdb (it should be noted that this structure was not accepted by the PDB and
149 the only certain information from the experiment is that this peptide forms
150 predominantly a three-stranded beta-sheet).
154 The CSA directory is divided into the BETANOVA and proteinA subdirectories for
155 these two molecules. In both cases the search results in a native-like structure
156 as the lowest-energy structure.
160 The example pertains to the 1FSD alpha/beta peptide. The directory run1 corresponds
161 to a "successful" run in which a native-like alpha/beta structure was obtained, while
162 the directory run2 to an "unsuccesful" one, in which a three-stranded non-native
163 beta-sheet was obtained as the lowest-energy structure. However, even this
164 native-like structure has a higher energy than the lowest energy structure found
165 so far (-77.518 kcal/mol; native-like). The NMR structure is in 1FSD.pdb.
169 The example pertains to 1IGD. This run has led to a non-native "negative" of
170 the protein, in which the beta-sheet is formed in the middle of the sequence and
171 not in the N- and the C-end. The energy is much higher than that of the lowest-energy
172 native structure, which is -745.355 kcal/mol. The native structure is in 1igd.pdb.
176 Another 1IGD example; this time the search resulted in the native structure.
177 However, the energy is higher than the lowest energy found (-747.433 kcal/mol).
183 [1] J. Lee, A. Liwo, H.A. Scheraga. Conformational space annealing and an
184 off-lattice united-residue force field: application to the 10-55 fragment of
185 staphylococcal protein A and to apo calbindin D9K. Proc. Natl. Acad. Sci. USA},
188 [2] J. Pillardy, C. Czaplewski, A. Liwo, J. Lee, D.R. Ripoll, R. Kazmierkiewicz,
189 St. Oldziej, W.J. Wedemeyer, K.D. Gibson, Y.A. Arnautova, J. Saunders,
190 Y.-J. Ye, H. A. Scheraga. Recent improvements in prediction of protein structure
191 by global optimization of a potential energy function. Proc. Natl. Acad. Sci.
192 USA, 2001, 98, 2329--2333.
196 5. Contact information
197 ----------------------
200 Faculty of Chemistry, University of Gdansk
201 ul. Sobieskiego 18, 80-952 Gdansk Poland.
202 phone: +48 58 345 0361
204 e-mail: adam@chem.univ.gda.pl
206 Dr. Cezary Czaplewski
207 Faculty of Chemistry, University of Gdansk
208 ul. Sobieskiego 18, 80-952 Gdansk Poland.
209 phone: +48 58 345 0361
211 e-mail: czarek@chem.univ.gda.pl
213 Dr. Stanislaw Oldziej
214 Baker Laboratory of Chemistry and Chemical Biology
216 Ithaca, NY 14853-1301, U.S.A.
217 phone: (607) 255 0556
219 e-mail: stan@scheraga2.chem.cornell.edu
221 Dr. Jaroslaw Pillardy
222 Baker Laboratory of Chemistry and Chemical Biology
224 Ithaca, NY 14853-1301, U.S.A.
225 phone: (607) 255 0556
227 e-mail: jp86@cornell.edu
230 Korea Institute for Advanced Study
231 207-43 Cheongryangri-dong Dongdaemun-gu
235 e-mail: jlee@kias.re.kr
237 Prepared by Adam Liwo, Cezary Czaplewski, and Stanislaw Oldziej, 9/1/03