Coevolution + Structure Prediction
Disclaimer: The following list is not intended to be a complete literature of coevolution history but only intended to showcase the milestones towards protein structure prediction from coevolutionary information. Typically the "first" manuscript or abstract@conference that demonstrated the idea. If you see anything missing, please alert us!
Using co-mutation data for structure prediction
1964 - C Yanofsky, V Horn, D Thorpe - Protein structure relationships revealed by mutational analysis - Link
Double mutations in MSA and mapping of co-evolving residues on 3D structure
1968 - "structure, function and evolution in proteins" (see session III) Link
Model to account for co-evolution
1970 - WM Fitch, E Markowitz - An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution - Link
Using co-variation in MSA to predict 3D structure
1991 - SA Benner, D Gerloff - Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases - Link
Using mutual-information to detect coevolution
1991 (for RNA) - DKY Chiu, T Kolodziejczak - Inferring consensus structure from nucleic acid sequences - Link
1992 (for Codons)- R Farber, A Lapedes, K Sirotkin - Determination of eukaryotic protein coding regions using neural networks and information theory - Link
1993 (for Proteins) - B Korber , R Farber , D Wolpert , A Lapedes - Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis - Link
Using correlation-matrix to detect coevolution
Statistical coupling analysis
1999 - Lockless SW, Ranaganathan R - Evolutionarily conserved pathways of energetic connectivity in protein families - Link
Recovering protein structures from sparse contact maps
1997 - contact map - Vendruscolo M, Kussell E, Domany E - Recovery of protein structure from contact maps - Link
1997 - sparse contact map - Skolnick J, Kolinski A, Ortiz AR. - MONSSTER: a method for folding globular proteins with a small number of distance restraints. Journal of molecular biology - Link
1999 - coevolution - Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. - Ab initio folding of proteins using restraints derived from evolutionary information - Link
Corrections
2007 - APC - SD Dunn, LM Wahl, GB Gloor - Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction - Link
Learning the MRF (or Potts models) for protein sequences to predict contacts
1997 - Partial correlation coefficient (diagional-normalized inverse-covariance) - Link
1999 - Approx. partition function using MCMC - Link
2005 - Heuristic approach (adding edges between high MI) - Abstract, Paper
2009 - Iterative message-passing algorithm - (DCA) - Link
2009 - Pseudolikelihood with group-sparsity - (GREMLIN) - Abstract, Paper
2011 - Inverse covariance - (mfDCA) - Link
2012 - Sparse inverse covariance - (PSICOV) - Link
2013 - Pseudolikelihood with L2 and APC - (plmDCA, GREMLIN) - Link, Link
2018 - Contrastive divergence (ccmgen) - Link
2018 - Boltzmann machines (bmDCA) - Link
2020 - Masked-language-modeling (Single-layer-attention) - Link
2021 - Autoregressive (arDCA) - Link
Learning MRFs across protein families
2020 - Neural potts model (explicitly learning potts models) - Link
2020 - BERT (implicitly learning potts models) - Link
2021 - MSA transformer (implicit) - Link
Using contacts derived from SCA contacts to predict protein structure
2008 - Fold enumeration - Link
Using contacts derived from MRF contacts to predict protein structure
Extract contacts from MRFs using NN
Others that need to be investigated:
Burger L., van Nimwegen E. Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comp. Biol. 2010;6:1–17.
https://pubmed.ncbi.nlm.nih.gov/3237684/