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

DOI10.1016/J.JCP.2014.07.024zbMATH Open1349.92108arXiv1401.4832OpenAlexW2048310584MaRDI QIDQ349541FDOQ349541

Authors: Magnus Ekeberg, Tuomo Hartonen, Erik Aurell 

Publication date: 5 December 2016

Published in: Journal of Computational Physics (Search for Journal in Brave)

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 parallelizable, as well as inherently faster on a single processor, at negligible difference in accuracy. We test the new incarnation of the method on 148 protein families from the Protein Families database (PFAM), one of the largest tests of this class of algorithms to date.

Full work available at URL: https://arxiv.org/abs/1401.4832

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zbMATH Keywords

pseudolikelihoodinferencePotts modelprotein structure predictioncontact mapdirect-coupling analysis

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Lattice systems (Ising, dimer, Potts, etc.) and systems on graphs arising in equilibrium statistical mechanics (82B20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Graphical models, exponential families, and variational inference
• Small-correlation expansions for the inverse Ising problem
• Adaptive cluster expansion for the inverse Ising problem: convergence, algorithm and tests

Cited In (7)

• High-dimensional structure learning of binary pairwise Markov networks: a comparative numerical study
• Selection originating from protein stability/foldability: relationships between protein folding free energy, sequence ensemble, and fitness
• Genome-wide covariation in SARS-CoV-2
• Inference of RNA structural contacts by direct coupling analysis
• Maximum-likelihood estimation of the statistical distribution of Smith- Waterman local sequence similarity scores
• Optimal regularizations for data generation with probabilistic graphical models
• Comparison of two algorithms of direct coupling analysis of protein

Uses Software

• PSICOV
• PconsC
• Pfam

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