Protein threading: from mathematical models to parallel implementations

DOI10.1287/IJOC.1040.0092MaRDI QIDQ2890440zbMATH OpenOpenAlexFDO

Authors Rumen Andonov, Stefan Balev, Nicola Yanev

Publication date 8 June 2012

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

Full work available at URL https://doi.org/10.1287/ijoc.1040.0092

zbMATH Keywords

linear programminginteger programmingparallel algorithmslarge-scale problemsnetwork optimizationprotein-threading problem

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Deterministic network models in operations research (90B10) Integer programming (90C10) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

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Cited in

(12)

• A new graph theoretic approach for protein threading
• A New Constraint Solver for 3D Lattices and Its Application to the Protein Folding Problem
• Parallel evolution strategy on grids for the protein threading problem
• Integer Linear Programming in Computational Biology
• An algorithm for simultaneous backbone threading and side-chain packing
• An algorithm for simultaneous backbone threading and side-chain packing
• Protein threading by linear programming: theoretical analysis and computational results
• Some operations research methods for analyzing protein sequences and structures
• Local protein threading by mixed integer programming
• Protein threading by linear programming
• Lagrangian approaches for a class of matching problems in computational biology
• Mathematical programming in computational biology: an annotated bibliography

Describes a project that uses

Uses Software

• RAPTOR
• CPLEX

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