* 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