Distance geometry optimization for protein structures

DOI10.1023/A:1008380219900zbMath0944.92012OpenAlexW1856811566MaRDI QIDQ1969508

Yanyan Li

Publication date: 26 April 2000

Published in: Journal of Global Optimization (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1023/a:1008380219900

zbMATH Keywords

distance constraintsprotein structuresdgsol code

Mathematics Subject Classification ID

Numerical optimization and variational techniques (65K10) Distance geometry (51K99) Biochemistry, molecular biology (92C40)

Related Items (35)

Euclidean distance matrix completion problems ⋮ Solving molecular distance geometry problems by global optimization algorithms ⋮ An improved hybrid global optimization method for protein tertiary structure prediction ⋮ An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data ⋮ A symmetry-based splitting strategy for discretizable distance geometry problems ⋮ The discretizable distance geometry problem ⋮ Recent advances on the interval distance geometry problem ⋮ A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem ⋮ Hyperbolic smoothing and penalty techniques applied to molecular structure determination ⋮ On the uniqueness of Euclidean distance matrix completions. ⋮ Least-squares approximations in geometric buildup for solving distance geometry problems ⋮ Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm ⋮ A DC programming approach for sensor network localization with uncertainties in anchor positions ⋮ Discretization orders and efficient computation of Cartesian coordinates for distance geometry ⋮ New error measures and methods for realizing protein graphs from distance data ⋮ The discretizable molecular distance geometry problem ⋮ Semidefinite programming for discrete optimization and matrix completion problems ⋮ On the computation of protein backbones by using artificial backbones of hydrogens ⋮ An optimization approach to the problem of protein structure prediction ⋮ Molecular conformation search by distance matrix perturbations ⋮ Extending the geometric build-up algorithm for the molecular distance geometry problem ⋮ On the uniqueness of Euclidean distance matrix completions: the case of points in general position ⋮ Geometric algebra to describe the exact discretizable molecular distance geometry problem for an arbitrary dimension ⋮ An application of a global optimization parametrization method on macromolecular structure problem ⋮ Positive semidefinite relaxations for distance geometry problems. ⋮ Euclidean Distance Matrices and Applications ⋮ A new algorithm for the \(^K\)DMDGP subclass of distance geometry problems with exact distances ⋮ Unnamed Item ⋮ Solving Distance Geometry Problem with Inexact Distances in Integer Plane ⋮ Global optimization based on local searches ⋮ A Euclidean distance matrix model for protein molecular conformation ⋮ Global optimization based on local searches ⋮ Double variable neighbourhood search with smoothing for the molecular distance geometry problem ⋮ A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation ⋮ Constrained Best Euclidean Distance Embedding on a Sphere: A Matrix Optimization Approach

This page was built for publication: Distance geometry optimization for protein structures