Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets.

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ECOD: An Evolutionary Classification of Protein Domains (2014, methodology): “In order to extend distant evolutionary relationships beyond the SCOP superfamily level in ECOD, we apply state of the art homology-inference algorithms both developed in our group [19,20] as well as by others [21,22], manually analyze and verify the suggested homologous links, and incorporate findi”
HorA web server to infer homology between proteins using sequence and structural similarity (2009, methodology): “(19) for equations and references of these scores.”
COMPASS server for homology detection: improved statistical accuracy, speed and functionality (2009, methodology): “COMPASS has been successfully used by our group and other researchers for both prediction of protein structure and function [e.g. (23,24)] and evolutionary analysis [e.g. (12,25,26)].”