Maxent-stress optimization of 3D biomolecular models

DOI10.4230/LIPICS.ESA.2017.70MaRDI QIDQ5111761zbMATH OpenFDO

Authors Michael Wegner, Oskar Taubert, Alexander Schug, Henning Meyerhenke

Publication date 27 May 2020

Full work available at URL https://arxiv.org/abs/1706.06805

zbMATH Keywords

distance geometryprotein structure determination3D graph drawingmaxent-stress optimization

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Graph theory (including graph drawing) in computer science (68R10) Computer graphics; computational geometry (digital and algorithmic aspects) (68U05) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

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Cites work

• scientific article; zbMATH DE number 2188749 (Why is no real title available?)
• scientific article; zbMATH DE number 3080144 (Why is no real title available?)
• A Distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Conformation
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• An SDP-based divide-and-conquer algorithm for large-scale noisy anchor-free graph realization
• Distance Geometry
• Distance geometry optimization for protein structures
• Double variable neighbourhood search with smoothing for the molecular distance geometry problem
• Drawing large graphs by multilevel maxent-stress optimization
• Eigensolver Methods for Progressive Multidimensional Scaling of Large Data
• Euclidean distance geometry and applications
• Faster Force-Directed Graph Drawing with the Well-Separated Pair Decomposition
• Global Continuation for Distance Geometry Problems
• Large-Scale Molecular Optimization from Distance Matrices by a D.C. Optimization Approach
• Lean algebraic multigrid (LAMG): fast graph Laplacian linear solver
• Maxent-stress optimization of 3D biomolecular models
• Metaheuristics. From design to implementation.
• Solving large scale molecular distance geometry problems by a smoothing technique via the Gaussian transform and D.C. programming
• Using a distributed SDP approach to solve simulated protein molecular conformation problems

Cited in

(3)

• A Euclidean distance matrix model for protein molecular conformation
• A probabilistic approach to determining biological structure: integrating uncertain data sources
• Maxent-stress optimization of 3D biomolecular models

Describes a project that uses

Uses Software

• NetworKit
• DISCO
• LAMG

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