Protein topology from predicted residue contacts

Protein Sci. 2012 Feb;21(2):299-305. doi: 10.1002/pro.2002. Epub 2011 Dec 21.


Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Computational Biology* / methods
  • Models, Biological
  • Models, Molecular
  • Models, Statistical*
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Protein Binding / genetics
  • Protein Binding / physiology
  • Protein Conformation*
  • Protein Folding
  • Protein Interaction Domains and Motifs / genetics
  • Protein Interaction Domains and Motifs / physiology*
  • Protein Structure, Secondary
  • Proteins / chemistry
  • Sequence Alignment
  • Sequence Homology, Amino Acid


  • Proteins