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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)
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Abstract

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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

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