Protein Engineering, Vol. 13, No. 11, 745-752,
November 2000
© 2000 Oxford University Press
ProSup: a refined tool for protein structure alignment
1 Center for Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringer Str. 3, A-5020 Salzburg and 3 ProCeryon Biosciences GmbH, Jakob-Haringer Str. 3, A-5020 Salzburg, Austria
We investigated and optimized a method for structure comparison which is based on rigid body superimposition. The method maximizes the number of structurally equivalent residues while keeping the root mean square deviation constant. The resulting number of equivalent residues then provides an adequate similarity measure, which is easy to interpret. We demonstrate that the approach is able to detect remote structural similarity. We show that the number of equivalent residues is a suitable measure for ranking database searches and that the results are in good agreement with expert knowledge protein structure classification. Structure comparison frequently has multiple solutions. The approach that we use provides a range of alternative alignments rather a single solution. We discuss the nature of alternative solutions on several examples.
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