Homologous proteins
CLICK and the other methods (HOMSTRAD, MUSTANG, Geometric Hashing, SALIGN, and DALI) were tested for alignment accuracy on a dataset of structures of pairs of homologous proteins. 9537 pair-wise alignments implied by the HOMSTRAD database of multiple alignments were used for this dataset. In all, this dataset comprised of 3454 structures and is available at here.
Difficult cases of aligning homologous protein pairs
This second dataset is used to quantitatively assess the performance of CLICK when structure similarity is low, as in the case of distant homologues. They include 64 pair-wise alignments from HOMSTRAD database with 30% < SO < 70% and RMSD>2.5Å.The alignment accuracy of CLICK is compared to results obtained from other methods on this dataset.
Similar structure but different topology
This dataset includes 89 pair-wise alignments from circular permutations (5 pair-wises) {Andreeva et al., 2007;Grishin, 2001}, non-topological alignments (60 pair-wises) {Dror et al., 2003}, and swapped domains (24 pair-wises) {Andreeva et al., 2007;Liu and Eisenberg, 2002}. Here, CLICK is compared to the other sequence-order-independent methods. Structural similarities between proteins in this dataset could be indicative of evolutionary relationships between the proteins despite pronounced structural differences in fold (topology).
Proteins in different conformations
The structural alignments of alternative conformations produce a useful comparison of the structures that exhibit domain motion or rigid body shifts. A characterization of such motions may lead to an improved understanding of the relationship between structure and function. The structure comparisons of alterative conformations were carried out for 22 proteins. This included 20 proteins from the Hinge Atlas {Flores et al., 2007} and DNA Polymerase Beta proteins (2bpf, 2fmq), and maltodextrin binding proteins (1omp, 1anf).
RNA structure comparisons
A subset of 1275 pair-wise alignments was benchmarked by the SARA server. This subset contained alignments between 51 RNA structures each having between 19 and 157 nucleotide residues
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