Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design

DOI10.1007/s10878-005-1859-8zbMath1077.92019OpenAlexW1983562846MaRDI QIDQ2576440

Yanyan Li

Publication date: 13 December 2005

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

Full work available at URL: https://doi.org/10.1007/s10878-005-1859-8

zbMATH Keywords

optimizationstructure predictiondrug designde novo protein designin silico sequence selectionpeptide and protein design and discovery

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Combinatorial optimization (90C27) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Discrete location and assignment (90B80)

Related Items (4)

Protein structure optimization by side-chain positioning via beta-complex ⋮ On maximum ratio clique relaxations ⋮ Overcoming the Key Challenges in De Novo Protein Design: Enhancing Computational Efficiency and Incorporating True Backbone Flexibility ⋮ Novel formulations for the sequence selection problem in de novo protein design with flexible templates

Uses Software

• CPLEX
• alphaBB

Cites Work

• Unnamed Item
• Reformulating nonlinear combinatorial optimization problems for higher computational efficiency
• Complexity of uniqueness and local search in quadratic 0-1 programming
• A reformulation-linearization technique for solving discrete and continuous nonconvex problems
• A Linearization Procedure for Quadratic and Cubic Mixed-Integer Problems
• Improved Linear Integer Programming Formulations of Nonlinear Integer Problems

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