MD-jeep: an implementation of a branch and prune algorithm for distance geometry problems. 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).
Keywords for this software
References in zbMATH (referenced in 9 articles )
Showing results 1 to 9 of 9.
- Liberti, Leo; Masson, Beno^ıt; Lee, Jon; Lavor, Carlile; Mucherino, Antonio: On the number of realizations of certain Henneberg graphs arising in protein conformation (2014)
- Liberti, Leo; Lavor, Carlile; Mucherino, Antonio: The discretizable molecular distance geometry problem seems easier on proteins (2013)
- Lima, Rodrigo S.; Martínez, J.M.: Solving molecular distance geometry problems using a continuous optimization approach (2013)
- Lavor, Carlile; Liberti, Leo; Maculan, Nelson; Mucherino, Antonio: Recent advances on the discretizable molecular distance geometry problem (2012)
- Lavor, Carlile; Liberti, Leo; Maculan, Nelson; Mucherino, Antonio: The discretizable molecular distance geometry problem (2012)
- Mucherino, A.; Lavor, C.; Liberti, L.: The discretizable distance geometry problem (2012)
- Lavor, C.; Mucherino, A.; Liberti, L.; Maculan, N.: On the computation of protein backbones by using artificial backbones of hydrogens (2011)
- Fukuda, Komei (ed.); van der Hoeven, Joris (ed.); Joswig, Michael (ed.); Takayama, Nobuki (ed.): Mathematical software -- ICMS 2010. Third international congress on mathematical software, Kobe, Japan, September 13--17, 2010. Proceedings (2010)
- Mucherino, Antonio; Liberti, Leo; Lavor, Carlile: MD-jeep: an implementation of a branch and prune algorithm for distance geometry problems (2010)