Predicting accurate contacts in thousands of Pfam domain families using PconsC3

Mirco Michel, Marcin J. Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson

Abstract: A few years ago it was shown that by using a maximum entropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i.e. are too small for such contact prediction methods.