Two programs for comparing proteins that conform to the coiled-coil structure are given. The first tool Matcher aligns a coiled-coil protein to the seven positions of the heptad. The second tool 2DMatch uses the output of Matcher to compare the outer surface of two coiled-coil proteins. 2DMatch reports all identical clusters of amino acids on this outer surface. The importance of the algorithm stems from the fact that from an immunological point of view, these sites may correspond to cross-reactive epitopes, i.e. sites at which antibodies produced against one protein also bind to another conformationally similar protein. Frequently, when such proteins are examined for sequence identities, few linear stretches are found that could account for the observed cross-reactions. 2DMatch has been shown to give successful predictions, while taking only the (predicted) secondary structure of the proteins into account, and can be used even if the coordinates of their 3-dimensional structure are not known.
Takes protein sequences in GENTRANS format, and aligns them to the seven positions of the coiled-coil heptad.


Takes the output of Matcher on two protein sequences as input. Reports identical clusters of amino acids found on both proteins and predicted to lie on the outer surface of the structures.

Please direct your questions to:

Jeanette P. Schmidt, Polytechnic University. jps@pucs4.poly.edu

Tak C. Ip, Polytechnic University. takip@pucs4.poly.edu