ProSup: a refined tool for protein structure alignment

We investigated and optimized a method for structure comparison which is ba sed on rigid body superimposition. The method maximizes the number of struc turally equivalent residues while keeping the root mean square deviation co nstant. The resulting number of equivalent residues then provides an adequa te similarity measure, which is easy to interpret. We demonstrate that the approach is able to detect remote structural similarity. We show that the n umber of equivalent residues is a suitable measure for ranking database sea rches and that the results are in good agreement with expert knowledge prot ein structure classification. Structure comparison frequently has multiple solutions. The approach that we use provides a range of alternative alignme nts rather a single solution. We discuss the nature of alternative solution s on several examples.