Computational protein design as an optimization problem

DOI10.1016/j.artint.2014.03.005zbMath1407.92099OpenAlexW2082527422MaRDI QIDQ2453727

Steven Prestwich, George Katsirelos, Barry O'Sullivan, Isabelle André, Sophie Barbe, Jessica Davies, Thomas Schiex, Seydou Traoré, Simon de Givry, David Allouche

Publication date: 10 June 2014

Published in: Artificial Intelligence (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.artint.2014.03.005

zbMATH Keywords

quadratic programmingbioinformaticsinteger linear programmingconstraint optimizationmaximum satisfiabilitygraphical modelweighted constraint satisfaction problemsoft constraintsmaximum a posteriori inferencecost function networkscomputational protein designneighborhood substitutability

Mathematics Subject Classification ID

Integer programming (90C10) Quadratic programming (90C20) Protein sequences, DNA sequences (92D20) Problem solving in the context of artificial intelligence (heuristics, search strategies, etc.) (68T20)

Related Items (8)

Tractability-preserving transformations of global cost functions ⋮ Multi-language evaluation of exact solvers in graphical model discrete optimization ⋮ Multiple-choice knapsack constraint in graphical models ⋮ Virtual pairwise consistency in cost function networks ⋮ Approximate Counting with Deterministic Guarantees for Affinity Computation ⋮ Accelerating exact and approximate inference for (distributed) discrete optimization with GPUs ⋮ CCEHC: an efficient local search algorithm for weighted partial maximum satisfiability ⋮ Variable neighborhood search for graphical model energy minimization

Uses Software

• ToulBar2
• Zinc
• MiniMaxSat
• Biq Mac
• MaxHS
• mplp2
• Osprey

Cites Work

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• Biq Mac
• Arc consistency for soft constraints
• Solving weighted CSP by maintaining arc consistency
• High-order consistency in valued constraint satisfaction
• Solving Max-cut to optimality by intersecting semidefinite and polyhedral relaxations
• The design of the zinc modelling language
• Soft arc consistency revisited
• AND/OR search spaces for graphical models
• Reasoning from last conflict(s) in constraint programming
• Depth-first iterative-deepening: An optimal admissible tree search
• Branching rules revisited
• Mini-buckets
• GAC Via Unit Propagation
• Solving (Weighted) Partial MaxSAT through Satisfiability Testing
• Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming
• A Computational Study of Search Strategies for Mixed Integer Programming
• New Upper Bounds for Maximum Satisfiability
• Solving Wind Farm Layout Optimization with Mixed Integer Programming and Constraint Programming
• Exploiting the Power of mip Solvers in maxsat

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