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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
  • Map of co-evolving residues on 3D structure
  • 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 AA) - 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 
    • 1994 -Göbel U, Sander C, Schneider R, Valencia A - Correlated mutations and residue contacts in proteins - Link
    • 1994 - Taylor WR, Hatrick K - Compensating changes in protein multiple sequence alignments - Link
  • 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
    • 1999 - Approx. partition function using MCMC - Link
    • 2005 - Heuristic approach (adding edges between high MI) - Link
    • 2009 - Iterative message-passing algorithm - (DCA) - Link
    • 2009 - Pseudolikelihood with group-sparsity - (GREMLIN) - Link
    • 2011 - Inverse covariance - (mfDCA) - Link
    • 2012 - Sparse inverse covariance - (PSICOV) - Link
    • 2013 - Pseudolikelihood with L2 and APC - (plmDCA, GREMLIN) - LinkLink
    • 2018 - Contrastive divergence - 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
    • 2011 - Fold enumeration - Link
    • 2011 - CNS - (DCAfold/EVfold) - LinkLink
    • 2014 - Fragments (Fragfold/Rosetta) - Link, Link
  • Extract contacts from MRFs using NN
    • 2015 - CNN on Contacts - MetaPSICOV - Link
    • 2016 - CNN on MRF -Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images - Link
    • 2017 - ResNet on contacts - Jinbo Xu - Link
    • 2018 - ResNet on MRF - AlphaFold - LinkLink
  • 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.
    • Altschuh D., Lesk A.M., Bloomer A.C., Klug A. Correlation of coordinated amino-acid substitutions with function in tobamoviruses. Protein Eng. 1987;1:228.