MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems

Antonio Mucherino; Leo Liberti; Carlile Lavor

doi:10.1007/978-3-642-15582-6_34

MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems

Antonio Mucherino
, Leo Liberti
, Carlile Lavor

INRIA Institut National de Recherche en Informatique et en Automatique
Department of Applied Mathematics
University of Campinas (UNICAMP)

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

23 Citations (Scopus)

Résumé

We present MD-jeep, an implementation of a Branch & Prune (BP) algorithm, which we employ for the solution of distance geometry problems related to molecular conformations. We consider the problem of finding the conformation of a molecule from the distances between some pairs of its atoms, which can be estimated by experimental techniques. We reformulate this problem as a combinatorial optimization problem, and describe a branch and prune solution strategy. We discuss its software implementation, and its complexity in terms of floating-point operations and memory requirements. MD-jeep has been developed in the C programming language. The sources of the presented software are available on the Internet under the GNU General Public License (v.2).

langue originale	Anglais
titre	Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings
Editeur	Springer Verlag
Pages	186-197
Nombre de pages	12
ISBN (imprimé)	3642155812, 9783642155819
Les DOIs	https://doi.org/10.1007/978-3-642-15582-6_34
état	Publié - 1 janv. 2010

Série de publications

Nom	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	6327 LNCS
ISSN (imprimé)	0302-9743
ISSN (Electronique)	1611-3349

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10.1007/978-3-642-15582-6_34

Contient cette citation

Mucherino, A., Liberti, L., & Lavor, C. (2010). MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems. Dans Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings (p. 186-197). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol 6327 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-642-15582-6_34

Mucherino, Antonio ; Liberti, Leo ; Lavor, Carlile. / MD-jeep : An implementation of a Branch and Prune algorithm for distance geometry problems. Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings. Springer Verlag, 2010. p. 186-197 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "We present MD-jeep, an implementation of a Branch \& Prune (BP) algorithm, which we employ for the solution of distance geometry problems related to molecular conformations. We consider the problem of finding the conformation of a molecule from the distances between some pairs of its atoms, which can be estimated by experimental techniques. We reformulate this problem as a combinatorial optimization problem, and describe a branch and prune solution strategy. We discuss its software implementation, and its complexity in terms of floating-point operations and memory requirements. MD-jeep has been developed in the C programming language. The sources of the presented software are available on the Internet under the GNU General Public License (v.2).",

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Mucherino, A, Liberti, L & Lavor, C 2010, MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems. Dans Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), VOL. 6327 LNCS, Springer Verlag, p. 186-197. https://doi.org/10.1007/978-3-642-15582-6_34

MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems. / Mucherino, Antonio; Liberti, Leo; Lavor, Carlile.
Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings. Springer Verlag, 2010. p. 186-197 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol 6327 LNCS).

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

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N2 - We present MD-jeep, an implementation of a Branch & Prune (BP) algorithm, which we employ for the solution of distance geometry problems related to molecular conformations. We consider the problem of finding the conformation of a molecule from the distances between some pairs of its atoms, which can be estimated by experimental techniques. We reformulate this problem as a combinatorial optimization problem, and describe a branch and prune solution strategy. We discuss its software implementation, and its complexity in terms of floating-point operations and memory requirements. MD-jeep has been developed in the C programming language. The sources of the presented software are available on the Internet under the GNU General Public License (v.2).

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Mucherino A, Liberti L, Lavor C. MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems. Dans Mathematical Software, ICMS 2010 - Third International Congress on Mathematical Software, Proceedings. Springer Verlag. 2010. p. 186-197. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-15582-6_34

MD-jeep: An implementation of a Branch and Prune algorithm for distance geometry problems

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