Protein structure optimization by side-chain positioning via beta-complex

DOI10.1007/S10898-012-9886-3zbMATH Open1277.90166OpenAlexW2003237067MaRDI QIDQ367168FDOQ367168

D.-S. Kim, Joonghyun Ryu

Publication date: 26 September 2013

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

Full work available at URL: https://doi.org/10.1007/s10898-012-9886-3

zbMATH Keywords

optimalheuristicinteger linear programmingVoronoi diagrambeta-complexBetaSCPprotein designprotein structure optimizationquasi-triangulationRASProtamerSCWRL

Mathematics Subject Classification ID

Approximation methods and heuristics in mathematical programming (90C59) Applications of mathematical programming (90C90) Integer programming (90C10)

Cites Work

• A semidefinite programming approach to side chain positioning with new rounding strategies
• Title not available (Why is that?)
• Global minimum potential energy conformations of small molecules
• Title not available (Why is that?)
• Protein conformation of a lattice model using tabu search
• Region-expansion for the Voronoi diagram of 3D spheres
• Three-dimensional alpha shapes
• Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design
• Title not available (Why is that?)
• Title not available (Why is that?)
• Side Chain-Positioning as an Integer Programming Problem
• Algebraic and spectral properties of some quasiorthogonal polynomials encountered in quantum radiation
• The smallest enclosing ball of balls
• Research in Computational Molecular Biology
• Novel formulations for the sequence selection problem in de novo protein design with flexible templates
• Computational Science and Its Applications – ICCSA 2004
• Euclidean Voronoi diagram of 3D balls and its computation via tracing edges
• Quasi-worlds and quasi-operators on quasi-triangulations

Cited In (4)

• \(\alpha\)-concave hull, a generalization of convex hull
• Recent advances on the interval distance geometry problem
• Side Chain-Positioning as an Integer Programming Problem
• Research in Computational Molecular Biology

Uses Software

• Miniball
• CHARMM
• BetaSCP
• SCWRL4
• RASP
• QTFier

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