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The analysis of alignments of functionally equivalent proteins can reveal regularities such as correlated positions or residue patterns which are important to ensure a specific fold and various cellular functions. Many approaches are found in the literature which try to identify correlated positions to predict the residues that are close to each other in the three-dimensional folded structure. However, the quality of the predictions remains disappointing. One of the problems is that thedoi:10.1109/bibe.2006.253333 dblp:conf/bibe/KeimOTN06 fatcat:au5s53yhqvcppc3mnrggswmebi