ConFind is a tool for finding position pairs on proteins that are "in contact" – i.e., are such that the amino-acid identity at one position likely influences the amino-acid identity at the other. Such position pairs are expect to co-vary evolutionarily and to have non-negligeable thermodynamic coupling energies.
ConFind is written in C++, on top of the general-purpose MSL library. MSL is available for free, under the terms of the GNU General Public License, as is ConFind. Click here to download ConFind as source code or a binary.
If you use ConFind in your research, feel free to cite any of these papers:
 "Sequence statistics of tertiary structural motifs reflect protein stability", F. Zheng, G. Grigoryan, PLoS ONE, 12(5): e0178272, 2017.
 "Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships", F. Zheng, J. Zhang, G. Grigoryan, Structure, 23(5): 961-971, 2015.