A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies

DOI10.1287/IJOC.1040.0096zbMath1239.90083OpenAlexW2097649955MaRDI QIDQ2890439

Carl Kingsford, Mona Singh, Bernard Chazelle

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.1040.0096

zbMATH Keywords

semidefinite programmingcomputational biologyside chain positioning

Mathematics Subject Classification ID

Semidefinite programming (90C22) Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Genetics and epigenetics (92D10)

Related Items (12)

Chromatic kernel and its applications ⋮ Introduction to QUBO ⋮ Mathematical programming in computational biology: an annotated bibliography ⋮ 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 ⋮ Efficient Use of Semidefinite Programming for Selection of Rotamers in Protein Conformations ⋮ Sublinear time width-bounded separators and their application to the protein side-chain packing problem ⋮ A cost-aggregating integer linear program for motif finding ⋮ Some operations research methods for analyzing protein sequences and structures ⋮ An exact algorithm for side-chain placement in protein design ⋮ A strictly contractive Peaceman-Rachford splitting method for the doubly nonnegative relaxation of the minimum cut problem ⋮ Integer Linear Programming in Computational Biology

Uses Software

• SDPA

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