  Predicting three dimensional residue-residue contacts from evolutionary
information in protein sequences was attempted already in the early 1990s.
However, contact prediction accuracies of methods evaluated in CASP experiments
before CASP11 remained quite low, typically with $<20$% true positives.
Recently, contact prediction has been significantly improved to the level that
an accurate three dimensional model of a large protein can be generated on the
basis of predicted contacts. This improvement was attained by disentangling
direct from indirect correlations in amino acid covariations or cosubstitutions
between sites in protein evolution. Here, we review statistical methods for
extracting causative correlations and various approaches to describe protein
structure, complex, and flexibility based on predicted contacts.
