MatchMaker Results

The test cases involve structures with low pairwise sequence identity:

The MatchMaker tool in Chimera constructs a sequence alignment and superimposes the structures accordingly. As of version 1.2129 (June 2005), secondary structure can be used to help construct the alignment, which allows pairs with lower percent identity to be superimposed correctly. However, MatchMaker does not handle/detect circular permutations. Results from using MatchMaker with the default settings in version 1.2129:

Results are about as good as with the superposition servers. The multiple superposition here is not truly multiple, but constructed from pairwise matches of 4enl and 1nu5 to the reference structure, 2mnr.

December 2005: Results are the same with Chimera version 1.2184 and the newer MatchMaker defaults (30% weighting of secondary structure score):


Elaine Meng / meng@cgl.ucsf.edu / home page