Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

@article{Ekeberg2014FastPM,
  title={Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences},
  author={Magnus Ekeberg and T. Hartonen and E. Aurell},
  journal={J. Comput. Phys.},
  year={2014},
  volume={276},
  pages={341-356}
}
Abstract Direct-coupling analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. In protein families of realistic size, this learning can only be done approximately, and there is a trade-off between inference precision and computational speed. We here show that an earlier introduced l 2 -regularized pseudolikelihood maximization method called plmDCA can be modified as to be easily… Expand
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