Efficient Use of Semidefinite Programming for Selection of Rotamers in Protein Conformations

DOI10.1287/ijoc.2014.0596zbMath1304.90224OpenAlexW2063249983MaRDI QIDQ2940065

Yuen-Lam Cheung, F. J. Burkowski, Henry Wolkowicz

Publication date: 26 January 2015

Published in: INFORMS Journal on Computing (Search for Journal in Brave)

Full work available at URL: https://semanticscholar.org/paper/ee8b85b0c81c841a6e8a22eea95d8db905a3cc6d

zbMATH Keywords

semidefinite programmingprotein structuresside chain positioning

Mathematics Subject Classification ID

Semidefinite programming (90C22) Applications of mathematical programming (90C90) Genetics and epigenetics (92D10)

Related Items (3)

Preprocessing and Regularization for Degenerate Semidefinite Programs ⋮ Validating numerical semidefinite programming solvers for polynomial invariants ⋮ Partial facial reduction: simplified, equivalent SDPs via approximations of the PSD cone

Uses Software

• SDPT3
• Chimera

Cites Work

• Solving semidefinite-quadratic-linear programs using SDPT3
• Behavioral measures and their correlation with IPM iteration counts on semi-definite programming problems
• Semidefinite programming relaxations for the quadratic assignment problem
• A recipe for semidefinite relaxation for \((0,1)\)-quadratic programming
• Semidefinite programming relaxations for the graph partitioning problem
• On Lagrangian Relaxation of Quadratic Matrix Constraints
• A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
• The trust region subproblem and semidefinite programming*
• Benchmarking optimization software with performance profiles.
• Computational experience with ill-posed problems in semidefinite programming

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