Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility

DOI10.1007/978-3-540-76784-8_4MaRDI QIDQ4607140zbMATH OpenOpenAlexFDO

Authors Christodoulos A. Floudas, Ho Ki Fung, Dimitrios Morikis, Martin S. Taylor, Li Zhang

Publication date 12 March 2018

Published in Applied Optimization (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-540-76784-8_4

zbMATH Keywords

de novo protein designbin variablesfold specificity stagetrue protein backbone flexibilityweighted average forcefield

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

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• scientific article; zbMATH DE number 2130520

Cites work

• scientific article; zbMATH DE number 976325 (Why is no real title available?)
• A Linearization Procedure for Quadratic and Cubic Mixed-Integer Problems
• A reformulation-linearization technique for solving discrete and continuous nonconvex problems
• Ab initio tertiary structure prediction of proteins
• Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in De Novo protein design
• Deterministic global optimization. Theory, methods and applications
• Improved Linear Integer Programming Formulations of Nonlinear Integer Problems
• Novel formulations for the sequence selection problem in de novo protein design with flexible templates
• Reformulating nonlinear combinatorial optimization problems for higher computational efficiency

Cited in

(1)

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

Describes a project that uses

Uses Software

• CYANA
• DYANA
• TINKER
• CPLEX

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