Molecular distance geometry methods: from continuous to discrete

DOI10.1111/j.1475-3995.2009.00757.xzbMath1219.90177WikidataQ62562185 ScholiaQ62562185MaRDI QIDQ3087839

Leo Liberti, Antonio Mucherino, Nelson F. Maculan, Carlile C. Lavor

Publication date: 17 August 2011

Published in: International Transactions in Operational Research (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1111/j.1475-3995.2009.00757.x

zbMATH Keywords

optimization; distance geometry; protein conformation

Mathematics Subject Classification ID

90C35: Programming involving graphs or networks

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Cites Work

• Unnamed Item
• Unnamed Item
• A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
• Solving molecular distance geometry problems by global optimization algorithms
• Theory of semidefinite programming for sensor network localization
• Rigid versus unique determination of protein structures with geometric buildup
• Combining variable neighborhood search and estimation of distribution algorithms in the protein side chain placement problem
• Extending the geometric build-up algorithm for the molecular distance geometry problem
• Double variable neighbourhood search with smoothing for the molecular distance geometry problem
• Isotropic effective energy simulated annealing searches for low energy molecular cluster states
• A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing
• Solving spread spectrum radar polyphase code design problem by tabu search and variable neighbourhood search.
• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• Solving large scale molecular distance geometry problems by a smoothing technique via the Gaussian transform and D.C. programming
• Global optimization of mixed-integer nonlinear programs: a theoretical and computational study
• An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
• Application of deterministic low-discrepancy sequences in global optimization
• Remarks to Maurice Frechet's article ``Sur la definition axiomatique d'une classe d'espaces vectoriels distancies applicables vectoriellement sur l'espace de Hilbert
• An Alternating Projection Algorithm for Computing the Nearest Euclidean Distance Matrix
• Branching and bounds tighteningtechniques for non-convex MINLP
• A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem
• A Distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Conformation
• Rigid and Flexible Frameworks
• Conditions for Unique Graph Realizations
• Global Continuation for Distance Geometry Problems
• Large-Scale Molecular Optimization from Distance Matrices by a D.C. Optimization Approach
• The Molecule Problem: Exploiting Structure in Global Optimization
• The Effective Energy Transformation Scheme as a Special Continuation Approach to Global Optimization with Application to Molecular Conformation