Nathaniel Leibowitz, Zipora Y. Fligelman, Ruth Nussinov, Haim J. Wolfson
Abstract
A Multiple Structural Alignment
algorithm is presented. The algorithm accepts an ensemble of protein
structures and finds the largest substructure (core) of C-alpha
atoms whose geometric configuration appear in all the molecules
of the ensemble (core). Both the detection of this core and the
resulting structural alignment are done simultaneously. Other
large enough multi-structural superimpositions are detected as
well. Our method is based on the Geometric Hashing paradigm and
a superimposition clustering technique which represents superimpositions
by sets of matching atoms. The algorithm proved to be efficient
on real data in a series of experiments. The same method can be
applied to any ensemble of molecules (not necessarily proteins)
since our basic technique is sequence order independent.
Keywords
Multiple structural alignment; Geometric Hashing; invariants;
structural core; transformation clustering.