Extending the geometric build-up algorithm for the molecular distance geometry problem
Information Processing Letters
MD-jeep: an implementation of a branch and prune algorithm for distance geometry problems
ICMS'10 Proceedings of the Third international congress conference on Mathematical software
An SDP-Based Divide-and-Conquer Algorithm for Large-Scale Noisy Anchor-Free Graph Realization
SIAM Journal on Scientific Computing
On the computation of protein backbones by using artificial backbones of hydrogens
Journal of Global Optimization
The discretizable molecular distance geometry problem
Computational Optimization and Applications
A discrete search algorithm for finding the structure of protein backbones and side chains
International Journal of Bioinformatics Research and Applications
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An updated geometric build-up algorithm is developed for solving the molecular distance geometry problem with a sparse set of inter-atomic distances. Different from the general geometric build-up algorithm, the updated algorithm re-computes the coordinates of the base atoms whenever necessary and possible. In this way, the errors introduced in solving the algebraic equations for the determination of the coordinates of the atoms are controlled in the intermediate computational steps. The method for re-computing the coordinates of the base atoms based on the estimation on the root-mean-square deviation (RMSD) is described. The results of applying the updated algorithm to a set of protein structure problems are presented. In many cases, the updated algorithm solves the problems with high accuracy when the results of the general algorithm are inadequate.