Abstract
In this paper, we propose a constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA (“Dynamics algorithm for NMR applications” [1]) an existing commercial application based on simulated annealing. For our test case, computation time for DYANA was more than six hours, whereas the method we propose produced similar results in 8 minutes, so we show that the application of Constraint Programming (CP) technology can greatly reduce computation time. This is a major advantage because this NMR technique generally demands multiple runs of structural computation.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Güntert, P., Mumenthaler, C., Wüthrich, K.: Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298 (1997)
Archer, M., Huber, R., Tavares, P., Moura, I., Moura, J.J., Carrondo, M.A., Sieker, L.C., LeGall, J., Romao, M.J.: Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure. J. Mol. Biol. 251(5), 690–702 (1995)
Goodfellow, B.J., Rusnak, F., Moura, I., Domke, T., Moura, J.J.G.: NMR determination of the global structure of the 113Cd derivative of Desulforedoxin: Investigation of the Hydrogen bonding pattern at the metal center. Protein Sc. 7, 928–937 (1998)
Press, V., Teukolsky, F.: Numerical Recipes in C, 2nd edn. Cambrige Univ. Press (1994)
Backofen, R.: Constraint Techniques for Solving the Protein Structure Prediction Problem, CP 1998. LNCS, vol. 1520, pp. 72–86. Springer, Heidelberg (1998)
Leishman, S., Gray, P.M.D., Fothergill, J.E.: ASSASSIN: A Constraint Based Assignment System for Protein 2D Nuclear Magnetic Resonance, Applications and Innovations in Expert Systems II. In: Milne, R., Montgomery, A. (eds.) Proceedings of Expert Systems 94, Cambridge, pp. 263–280 (1994)
Beldiceanu, N., Contejean, E.: Introducing Global Constraints in CHIP. Mathl. Comp. Modelling 20(12), 97–123 (1994)
Zimmerman, D.E., Kulikowski, C.A., Montelione, G.T.: A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra. Ismb 1, 447–55 (1993)
Hecht, S., Collins, S.: Three-dimensional structure of the complexes between bovine chymotrypsinogen *A and two recombinant variants of human pancreatic secretory trypsin inhibitor (*Kazal-Type). J. Mol. Biol. 220, 711 (1991)
Marquart, M., Walter, J., Deisenhofer, J., Bode, W., Huber, R.: The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr., Sect. B 39, 480 (1983)
Bushnell, G.W., Louie, G.V., Brayer, G.D.: High-Resolution Three-Dimensional Structure of Horse Heart Cytochrome C. J.Mol.Biol. 214, 585 (1990)
Revesz, P.: Refining Restriction Enzyme Genome Maps. Constraints 2, 361 (1997)
Sam-Haroud, D., Faltings, B.: Consistency Techniques for Continuous Constraints. Constraints 1, 85 (1996)
Cheng, B., Choi, K., Lee, J., Wu, J.: Increasing Constraint Propagation by Redundant Modeling: an Experience Report. Constraints 4, 167 (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Krippahl, L., Barahona, P. (1999). Applying Constraint Programming to Protein Structure Determination. In: Jaffar, J. (eds) Principles and Practice of Constraint Programming – CP’99. CP 1999. Lecture Notes in Computer Science, vol 1713. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-48085-3_21
Download citation
DOI: https://doi.org/10.1007/978-3-540-48085-3_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-66626-4
Online ISBN: 978-3-540-48085-3
eBook Packages: Springer Book Archive