Least-squares approximations in geometric buildup for solving distance geometry problems
This article further investigates some theoretical and computational issues of the geometric buildup algorithm proposed by \textit{A. Sit, Z. Wu} and \textit{X. Yuan} [Bull. Math. Biol. 71, No. 8, 1914--1933 (2009; Zbl 1180.92029)] for the solution of the distance geometry problem with sparse and inexact distances. This problem is derived from the protein modeling problem, where \(n\) atoms with their distances \(d_{ij}\) under the Euclidean norm are given and we seek their coordinates. The algorithm repeatedly uses a least-squares approximation to determine the position of an undetermined atom, using the distances from this atom to a set of previously determined ones. The least-squares approximation, obtained from the singular value decomposition of a distance-induced matrix, can find the best possible position for the atom, even if the distances have small errors, as they usually do in practice, and therefore make the geometric buildup algorithm more stable than its previous versions that relied on linear system solvers. In this paper, the authors estimate its numerical errors and prove some of its key mathematical properties. They also present some numerical results with varying some of the parameters in the algorithm and show how they may be used to improve its performance and computational accuracy.
- A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation
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- Distance geometry methods for protein structure determination
- A least-squares approach for discretizable distance geometry problems with inexact distances
- Rigid versus unique determination of protein structures with geometric buildup
- A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
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- An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
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