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Fast optimization of statistical potentials for structurally constrained phylogenetic models

Abstract : Background: Statistical approaches for protein design are relevant in the field of molecular evolutionary studies. In recent years, new, so-called structurally constrained (SC) models of protein-coding sequence evolution have been proposed, which use statistical potentials to assess sequence-structure compatibility. In a previous work, we defined a statistical framework for optimizing knowledge-based potentials especially suited to SC models. Our method used the maximum likelihood principle and provided what we call the joint potentials. However, the method required numerical estimations by the use of computationally heavy Markov Chain Monte Carlo sampling algorithms.
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https://hal.archives-ouvertes.fr/hal-03459100
Contributor : Nicolas Lartillot Connect in order to contact the contributor
Submitted on : Tuesday, November 30, 2021 - 11:17:46 PM
Last modification on : Thursday, December 9, 2021 - 3:40:33 AM

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Cécile Bonnard, Claudia Kleinman, Nicolas Rodrigue, Nicolas Lartillot. Fast optimization of statistical potentials for structurally constrained phylogenetic models. BMC Evolutionary Biology, BioMed Central, 2009, 9 (1), pp.227. ⟨10.1186/1471-2148-9-227⟩. ⟨hal-03459100⟩

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