Accurate contact predictions for thousands of protein families using PconsC3

Abstract

Protein structure prediction was for decades one of the grand unsolved challenges in bioinformatics. 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 was 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 existing contact prediction methods. To extend accurate contact predictions to the thousands of smaller protein families we present PconsC3, an improved method for protein contact predictions that can be used for families with as little as 100 effective sequence members. We estimate that PconsC3 provides accurate contact predictions for up to 4646 Pfam domain families. In addition, PconsC3 outperforms previous methods significantly independent on family size, secondary structure content, contact range, or the number of selected contacts. This improvement translates into improved de-novo prediction of three-dimensional structures. PconsC3 is available as a web server and downloadable version at http://c3.pcons.net. The downloadable version is free for all to use and licensed under the GNU General Public License, version 2.