Compact optimization can outperform separation: a case study in structural proteomics

DOI10.1007/S10288-004-0036-8MaRDI QIDQ1762887zbMATH OpenOpenAlexFDO

Authors Robert D. Carr, Giuseppe Lancia

Publication date 11 February 2005

Published in 4OR (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10288-004-0036-8

zbMATH Keywords

linear programmingcombinatorial optimizationnumerical examplestraveling salesman problemseparation algorithmcontact mapcompact optimizationprotein foldsstructural proteomicssubtour-elimination

Mathematics Subject Classification ID

Numerical mathematical programming methods (65K05) Linear programming (90C05) Applications of mathematical programming (90C90) Protein sequences, DNA sequences (92D20) Combinatorial optimization (90C27)

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Cited in

(8)

• An effective compact formulation of the max cut problem on sparse graphs
• Mixed integer linear programming formulation techniques
• Some operations research methods for analyzing protein sequences and structures
• Deriving compact extended formulations via LP-based separation techniques
• Optimal Transitions for Targeted Protein Quantification: Best Conditioned Submatrix Selection
• A branch-and-cut algorithm for multiple sequence alignment
• Deriving compact extended formulations via LP-based separation techniques
• Mathematical programming in computational biology: an annotated bibliography

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