Hostname: page-component-8448b6f56d-cfpbc Total loading time: 0 Render date: 2024-04-25T00:06:40.529Z Has data issue: false hasContentIssue false
  • English
  • Français

Exploring the conformations of nucleic acids

Published online by Cambridge University Press:  07 November 2008

Marcel Turcotte ,
Guy Lapalme  and
François Major
Marcel Turcotte
Affiliation:
Laboratoire de biologie informatique et théorique, Département d'informatique et de Recherche Opérationnelle, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada (e-mail:turcotte@IRO.UMontreal.CA, lapalme@IRO.UMontreal.CA, major@IRO.UMontreal.CA)
Guy Lapalme
Affiliation:
Laboratoire de biologie informatique et théorique, Département d'informatique et de Recherche Opérationnelle, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada (e-mail:turcotte@IRO.UMontreal.CA, lapalme@IRO.UMontreal.CA, major@IRO.UMontreal.CA)
François Major
Affiliation:
Laboratoire de biologie informatique et théorique, Département d'informatique et de Recherche Opérationnelle, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada (e-mail:turcotte@IRO.UMontreal.CA, lapalme@IRO.UMontreal.CA, major@IRO.UMontreal.CA)
Rights & Permissions [Opens in a new window]

Abstract

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

This paper presents an application of functional programming in the field of molecular biology: exploring the conformations of nucleic acids. The Nucleic Acid three-dimensional structure determination problem (NA3D) and a constraint satisfaction algorithm are formally described. Prototyping and experimental development using the Miranda functional programming language, over the last four years, are discussed. A Prolog implementation has been developed to evaluate software engineering and performance criteria between functional and logic programming. A C++ implementation has been developed for distribution purpose and to solve large practical problems. This system, called MC-SYM for ‘Macromolecular Conformation by SYMbolic generation’, is used in more than 50 laboratories, including academic and government research centres and pharmaceutical companies.

Type
Research Article
Information
Journal of Functional Programming , Volume 5 , Issue 3 , July 1995 , pp. 443 - 460
Copyright
Copyright © Cambridge University Press 1995

References

Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. and Schneider, B. (1992) The nucleic acid database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63: 751–759.CrossRefGoogle ScholarPubMed
Bernstein, R., Koetzle, T. F., Williams, G. J., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The Protein Data Bank: A computer-based archival file for macromolecular structures. Eur. Biochem., 80: 319–324.Google Scholar
Blumenthal, L. M. (1970) Theory and Applications of Distance Geometry. Chelsea.Google Scholar
Brown, R. S., Dewan, J. C. and Klug, A. (1985) Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast Phenylalanine t-RNA. Biochemistry 24: 4785–4801.Google Scholar
Comarmond, M. B., Giege, R., Thierry, J. C., Moras, D. and Fischer, J. (1986) Three-dimensional structure of yeast t-RNA-As p. I.|Structure determination. Acta Crystallogr., Sect.B. 42: 272–280.CrossRefGoogle Scholar
Dincbas, M. (1986) Constraints, logic programming and deductive databases. In: France-Japan Artificial Intelligence and Computer Science Symposium.Google Scholar
Easterwood, T., Major, F., Malhotra, A. and Harvey, S. (1994) Orientation of transfer RNA in the ribosomal A and P sites. Nucl. Acids Res. 22(18): 3779–3786.CrossRefGoogle ScholarPubMed
Feeley, M., Lapalme, G. and Turcotte, M. (1994) Using Multilisp for solving constraint satisfaction problems: an application to nucleic acid 3D structure determination. Lisp and Symbolic Computation, 7: 85–100.CrossRefGoogle Scholar
Foucrault, M., Cedergren, R. and Major, F. (1995) Modeling the lead-activated ribozyme by intersection of conformational space. In preparation.Google Scholar
Frenkel, K. A. (1991) The human genome project and informatics. Comm. ACM 34(11): 41–51.CrossRefGoogle Scholar
Gautheret, D. and Cedergren, R. (1993) Modeling the three-dimensional structure of RNA. FASEB J. 7(1): 97–105.CrossRefGoogle ScholarPubMed
Gray, M. and Cedergren, R. (1993) The new age of RNA. FASEB J. 7(1): 4–6.Google Scholar
Hartel, P., Feeley, M., Alt, M. et al. (1994) Pseudoknot: a float-intensive benchmark for functional compilers. Submitted.Google Scholar
Hentenryck, P. (1989) Constraint Satisfaction in Logic Programming. MIT Press.Google Scholar
Hingerty, B. E., Brown, R. S. and Jack, A. (1978) Further refinement of the structure of yeast t-RNA-Phe. J. Mol. Biol. 124: 523.CrossRefGoogle Scholar
Leclerc, F., Cedergren, R. and Ellington, A. D. (1994) A three-dimensional model of the Rev-binding element of HIV-1 derived from analyses aptamers. Nature Structural Biology 1(5): 293–300.Google Scholar
Levitt, M. (1969) Detailed molecular model for transfer ribonucleic acid. Nature 224: 759–763.CrossRefGoogle ScholarPubMed
Major, F. (1995) Computer modeling of RNA 3-D structures. In: Molecular Biology and Biotechnology: a comprehensive desk reference. Meyers, Robert A. Ed. VCH Publishers, New York, NY.Google Scholar
Major, F., Gautheret, D. and Cedergren, R. (1993) Reproducing the three-dimensional structure of a transfer RNA molecule from structural constraints. Proc. Natl. Acad. Sci. (USA) 90: 9408–9412.CrossRefGoogle ScholarPubMed
Major, F., Lapalme, G. and Cedergren, R. (1991a) Domain Generating Functions for Solving Constraint Satisfaction Problems. J. Funct. Prog. 1(2): 213–227.Google Scholar
Major, F., Turcotte, M., Gautheret, D. et al. (1991b) The Combination of Symbolic and Numerical Computation for Three-Dimensional Modeling of RNA. Science 253: 1255–1260.CrossRefGoogle ScholarPubMed
Miranda System Manual (1989) Research Software Limited, Canterbury, UK.Google Scholar
Ousterhout, J. (1990) TCL: An embeddable command language. In: 1990 Winter USENIX Conference, pp. 133–146.Google Scholar
Pereira, F. and Warren, D. (1980) Definite clause grammars for natural language analysis – a survey of the formalism and comparisons with augmented transition networks. Artif. Intell. 14: 231–278.CrossRefGoogle Scholar
Quintus Prolog 3.1: Reference Pages (1991) Quintus, Palo Alto.Google Scholar
Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New-York.Google Scholar
Steinberg, S., Misch, A. and Sprinzl, M. (1993) Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 21: 3011–3015.CrossRefGoogle ScholarPubMed
Sussman, J. L., Holbrook, S. R., Warrant, R. W. et al. (1978) Crystal structure of yeast Phenylalanine t-RNA. I.crystallographic refinement. J. Mol. Biol. 123: 607–630.Google Scholar
Van Hentenryck, P. and Dincbas, M. (1986) Domains in logic programming. In: Proc. AAAI-86.Google Scholar
Watson, J. D., Hopkins, N. H., Roberts, J. W. et al. (1987) Molecular Biology of the Gene, Vols. I & II. Benjamin Cummings.Google Scholar
Westhof, E., Dumas, P. and Moras, D. (1988) Restrained refinement of two crystalline forms of yeast Aspartic acid and Phenylalanine transfer RNA crystals. Acta Crystallogr., Sect.A. 44: 112.CrossRefGoogle ScholarPubMed
Westhof, E. and Sundaralingam, M. (1986) Restrained refinement of the monoclinic form of yeast Phenylalanine transfer RNA. temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry 25: 4868.CrossRefGoogle ScholarPubMed
Submit a response

Discussions

No Discussions have been published for this article.