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Euclidean Distance Geometry and Applications
The theory of Euclidean distance geometry and its most important applications are surveyed, with special emphasis on molecular conformation problems.
The discretizable molecular distance geometry problem
It is shown that under a few assumptions usually satisfied in proteins, the MDGP can be formulated as a search in a discrete space and the DMDGP is NP-hard and a solution algorithm called Branch-and-Prune (BP) is proposed.
A Branch-and-Prune algorithm for the Molecular Distance Geometry Problem
A Branch-and-Prune algorithm is proposed for the solution of the Molecular Distance Geometry Problem, showing that under an additional requirement on the given distances this can be transformed to a combinatorial problem.
Decrease of the incidence of human and canine visceral leishmaniasis after dog vaccination with Leishmune in Brazilian endemic areas.
Distance Geometry: Theory, Methods, and Applications
This paper presents an Overview on Protein Structure Determintion by NMR - Historical and Future Perspectives of the Use of Distance Geometry Methods, and some of their applications in Molecular Modeling.
A Function to Test Methods Applied to Global Minimization of Potential Energy of Molecules
It is proved that the number of local minimizers of this function increases exponentially with the size of the problem, which characterizes the principal difficulty in minimizing molecular potential energy functions.
A continuous variable neighborhood search heuristic for finding the three-dimensional structure of a molecule
A GA-Simplex Hybrid Algorithm for Global Minimization of Molecular Potential Energy Functions
Experimental evidence shows that the global minimum of the potential energy of a molecule corresponds to its most stable conformation, which dictates its properties.
Molecular distance geometry methods: from continuous to discrete
Some continuous and discrete methods for solving some problems of molecular distance geometry involve a search in a continuous Euclidean space but sometimes the problem structure helps reduce the search to a discrete set of points.
Discretization orders for distance geometry problems
- C. Lavor, Jon Lee, Audrey St. John, Leo Liberti, A. Mucherino, M. Sviridenko
- Mathematics, Computer ScienceOptim. Lett.
- 1 April 2012
This work formalizes the decision problem of determining whether such an order exists for a given graph and shows that this problem is NP-complete in general and polynomial for fixed dimension K.