Online Structure Alignment Resources (April 2005; later additions as noted)

This list is not meant to be comprehensive, but includes a reasonably broad sample of sites I think are handy and convenient to use.

The test cases involve structures with low pairwise sequence identity:

Default settings generally used.

Note that the MatchMaker tool in Chimera performs a similar function: it constructs a sequence alignment and superimposes the structures accordingly. Secondary structure can be used to help construct the alignment, which allows pairs with lower percent identity to be superimposed correctly (see results from using MatchMaker).

Superposition Servers

Circularly Permuted Test System (May 2005)

Test structures: 1qq5 A chain (HAD) 3chy (CheY)

These are in different superfamilies according to SCOP, but it has been noted that the structures appear to be related by circular permutation (see paper by Ridder and Dijkstra). The active site residues are in about the same positions in 3D, although in different N→C orders. Selected active site residues (those in a column are aligned in 3D):

                loop 1     loop 2     loop 3     loop4       
   2-HAD X. autrophicus                                  *
                 D8         S114       K147      171SS---D176
   epoxide hydrolase M. musculus, H. sapiens        *
                 D9         T123       K160      184DD---N189
   CheY E. coli, S. typhimurium                     *
                D57         T87        K109       12DD13
superimposed manually MultiProt (~10-15 seconds)
(the choice with the most residues aligned
and as a tie-breaker, the lowest RMSD)
K2SA (~15-20 seconds)
(wrong, see log file)

The Multiprot results correctly place the corresponding active site residues together; the K2SA results are shifted over by one strand in the central sheet. NB: The K2SA server appears to be imposing sequential constraints even when I set the option to NOT do so... which would explain the failure on this test case.

Sources of Structure-Based Sequence Alignments

(which can then be used in Chimera's Multalign Viewer to match the corresponding structures) Listed here are Web servers that generate alignments from your input. Databases of precalculated alignments are listed elsewhere.
meng[at] / home page