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

DOI10.1016/j.jcp.2014.07.024zbMath1349.92108arXiv1401.4832OpenAlexW2048310584MaRDI QIDQ349541

Tuomo Hartonen, Magnus Ekeberg, Erik Aurell

Publication date: 5 December 2016

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

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

zbMATH Keywords

Potts modelinferenceprotein structure predictioncontact mapdirect-coupling analysispseudolikelihood

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)

Related Items

Optimal regularizations for data generation with probabilistic graphical models, Selection originating from protein stability/foldability: relationships between protein folding free energy, sequence ensemble, and fitness, High-dimensional structure learning of binary pairwise Markov networks: a comparative numerical study, Genome-wide covariation in SARS-CoV-2

Uses Software

• PSICOV
• PconsC
• Pfam

Cites Work

• Adaptive cluster expansion for the inverse Ising problem: convergence, algorithm and tests
• Graphical Models, Exponential Families, and Variational Inference
• Small-correlation expansions for the inverse Ising problem