Abstract
We present a declarative implementation in Constraint Logic Programming of the Protein Folding Problem, for models based on Face-Centered Cubes. Constraints are either used to encode the problem as a minimization problem or to prune the search space. In particular, we introduce constraints using secondary structure information.
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Backofen, R.: The protein structure prediction problem: A constraint optimization approach using a new lower bound. Constraints 6(2/3), 223–255 (2001)
Berrera, M., Molinari, H., Fogolari, F.: Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4(8) (2003)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000), http://www.rcsb.org/pdb/
Bonneau, R., Baker, D.: Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure 30, 173–189 (2001)
Carlsson, M., Ottosson, G., Carlson, B.: An Open-Ended Finite Domain Constraint Solver. In: Hartel, P.H., Kuchen, H. (eds.) PLILP 1997. LNCS, vol. 1292, pp. 191–206. Springer, Heidelberg (1997)
Crescenzi, P., Goldman, D., Papadimitrou, C., Piccolboni, A., Yannakakis, M.: On the complexity of protein folding. In: Proc. of STOC, pp. 597–603 (1998)
Dovier, A., Burato, M., Fogolari, F.: Using Secondary Structure Information for Protein Folding in CLP(FD). In: 11th International Workshop on Functional and (Constraint) Logic Programming. ENTCS, vol. 76 (2002)
Fogolari, F., Esposito, G., Viglino, P., Cattarinussi, S.: Modeling of polypeptide chains as C-α chains, C-α chains with C-β, and C-α chains with ellipsoidal lateral chains. Biophysical Journal 70, 1183–1197 (1996)
Marriott, K., Stuckey, P.J.: Programming with Constraints. The MIT Press, Cambridge (1998)
Miyazawa, S., Jernigan, R.L.: Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. Journal of Molecular Biology 256(3), 623–644 (1996)
Raghunathan, G., Jernigan, R.L.: Ideal architecture of residue packing and its observation in protein structures. Protein Science 6, 2072–2083 (1997)
Rost, B., Sander, C.: Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology 232, 584–599 (1993)
Shakhnovich, E., Mirny, L.: Protein folding theory: from lattice to all-atom models. Annual Review of Biophysics and Biomolecular Structure 30, 361–396 (2001)
Skolnick, J., Kolinski, A.: Computational studies of protein folding. Computing in Science and Engineering 3(5), 40–50 (2001)
Simons, K.T., Bonneau, R., Ruczinski, I., Baker, D.: Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins (suppl. 3), 171–176 (1999), http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php
Sterling, L., Shapiro, E.: The Art of Prolog, 2nd edn. The MIT Press, Cambridge (1997)
Swain, M.T., Kemp, G.J.L.: A CLP approach to the protein side-chain placement problem. In: Walsh, T. (ed.) CP 2001. LNCS, vol. 2239, pp. 479–493. Springer, Heidelberg (2001)
Swedish Institute for Computer Science. Sicstus Prolog Home Page, http://www.sics.se/sicstus/
Toma, T., Toma, S.: Folding simulation of protein models on the structure-based cubo-octahedral lattice with the Contact Interactions algorithm. Protein Science 8, 196–202 (1999)
Vendruscolo, M., Kussell, E., Domany, E.: Recovery of Protein Structure from Contact Maps. Folding and Design 2, 295–306 (1997)
Will, S.: Constraint-based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice Sebastia. In: Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E. (eds.) Proceedings of the Pacific Symposium on Biocomputing (2002)
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Dal Palù, A., Dovier, A., Fogolari, F. (2004). Protein Folding in CLP(\(\mathcal{FD}\)) with Empirical Contact Energies. In: Apt, K.R., Fages, F., Rossi, F., Szeredi, P., Váncza, J. (eds) Recent Advances in Constraints. CSCLP 2003. Lecture Notes in Computer Science(), vol 3010. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24662-6_14
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DOI: https://doi.org/10.1007/978-3-540-24662-6_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-21834-0
Online ISBN: 978-3-540-24662-6
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