Software For Distance Geometry
- DGSOL. It is based on the idea of approximating the penalty function with a sequence of smoother functions converging to the original objective function. It is usually used for performing comparisons to other newly proposed techniques, whose code is often not released. DGSOL solves distance geometry problems where a lower and an upper bound on the distances are available.
- MD-jeep. This software is based on a combinatorial reformulation of the distance geometry problem. A Branch & Prune algorithm is implemented for an efficient solution of the reformulated problem. It has been mainly applied to distance geometry problems related to protein molecules.
- Xplor-NIH. It has been particularly designed for solving instances of the problem in which the data come from NMR experiments, and it includes different functionalities. In particular, for the solution of the distance geometry problems, it makes use of heuristic methods (such as Simulated Annealing) and local search methods (such as Conjugate Gradient Minimization).
- TINKER. This is a package for molecular modeling and design. It includes many force fields for attempting the prediction of protein conformations from their chemical structure only. One of its functionalities, however, is to solve distance geometry problems.
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