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A new framework for computational protein design through cost function network optimization

Abstract : Motivation: The main challenge for structure-based computational protein design (CPD) remains the combinatorial nature of the search space. Even in its simplest fixed-backbone formulation, CPD encompasses a computationally difficult NP-hard problem that prevents the exact exploration of complex systems defining large sequence-conformation spaces.[br/] Results: We present here a CPD framework, based on cost function network (CFN) solving, a recent exact combinatorial optimization technique, to efficiently handle highly complex combinatorial spaces encountered in various protein design problems. We show that the CFN-based approach is able to solve optimality a variety of complex designs that could often not be solved using a usual CPD-dedicated tool or state-of-the-art exact operations research tools. Beyond the identification of the optimal solution, the global minimum-energy conformation, the CFN-based method is also able to quickly enumerate large ensembles of suboptimal solutions of interest to rationally build experimental enzyme mutant libraries.
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Seydou Traore, David Allouche, Isabelle André, Simon de Givry, George Katsirelos, et al.. A new framework for computational protein design through cost function network optimization. Bioinformatics, Oxford University Press (OUP), 2013, 29 (17), pp.2129-2136. ⟨10.1093/bioinformatics/btt374⟩. ⟨hal-01268153⟩

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