Novel formulations for the sequence selection problem in de novo protein design with flexible templates

DOI10.1080/10556780600882041MaRDI QIDQ5758166zbMATHOpenAlexFDO

Authors Ho Ki Fung, Martin S. Taylor, Christodoulos A. Floudas

Publication date 3 September 2007

Published in Optimization Methods \& Software (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1080/10556780600882041

zbMATH Keywords

optimizationstructure predictiondrug designde novo protein designpeptide and protein design and discovery\(in silico\) sequence selectionprotein backbone flexibility

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40)

Recommendations

• Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design
• Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility
• An exact algorithm for side-chain placement in protein design
• A New Constraint Solver for 3D Lattices and Its Application to the Protein Folding Problem
• scientific article; zbMATH DE number 2081008

Cites work

• scientific article; zbMATH DE number 976325 (Why is no real title available?)
• A reformulation-linearization technique for solving discrete and continuous nonconvex problems
• Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design

Cited in

(5)

• Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design
• Some experiences with solving semidefinite programming relaxations of binary quadratic optimization models in computational biology
• Protein structure optimization by side-chain positioning via beta-complex
• Global optimality conditions for quadratic \(0-1\) optimization problems
• Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility

Describes a project that uses

Uses Software

• CPLEX
• alphaBB

This page was built for publication: Novel formulations for the sequence selection problem in de novo protein design with flexible templates

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5758166)