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Levy RM , Haldane A , Flynn WF
Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness
Curr Opin Struct Biol. 2017 Apr;43 :55-62
PMID: 27870991    PMCID: PMC5869684    URL: https://www.ncbi.nlm.nih.gov/pubmed/27870991
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Abstract
Potts Hamiltonian models of protein sequence co-variation are statistical models constructed from the pair correlations observed in a multiple sequence alignment (MSA) of a protein family. These models are powerful because they capture higher order correlations induced by mutations evolving under constraints and help quantify the connections between protein sequence, structure, and function maintained through evolution. We review recent work with Potts models to predict protein structure and sequence-dependent conformational free energy landscapes, to survey protein fitness landscapes and to explore the effects of epistasis on fitness. We also comment on the numerical methods used to infer these models for each application.
Notes
1879-033x Levy, Ronald M Haldane, Allan Flynn, William F P50 GM103368/GM/NIGMS NIH HHS/United States R01 GM030580/GM/NIGMS NIH HHS/United States Journal Article Review England Curr Opin Struct Biol. 2017 Apr;43:55-62. doi: 10.1016/j.sbi.2016.11.004. Epub 2016 Nov 18.