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).
Keywords
- Protein Data Bank
- Penalty Function
- Binary Tree
- Atomic Position
- Molecular Conformation
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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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. In: Fukuda, K., Hoeven, J.v.d., Joswig, M., Takayama, N. (eds) Mathematical Software – ICMS 2010. ICMS 2010. Lecture Notes in Computer Science, vol 6327. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15582-6_34
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DOI: https://doi.org/10.1007/978-3-642-15582-6_34
Publisher Name: Springer, Berlin, Heidelberg
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