SSM

You can find the server here

1.1. User interface, on-line help, choice of parameters and databases
User-friendly. Allows to type a PDBID of a known structure or upload coordinates. One migh choose lowest acceptible match.
1.2.Interactive versus E-mail results or notification
interactive
1.3. Documentation, access to literature references
Paper describing method has not been publish yet, no information on the web page, but the aurhr of the server answers the question readily and swiftly.
1.4. Confidentality
I haven't found any information
1.5. Elapsed time between submission and results
Usually very fast (in seconds), longest obserable time was 5 minutes.
1.6. How long are the results kept on the server ?
No info

2.1. What information is reported for the hits?
It contains PDB ID of similar structure, z score,P score, RMSD, number of equivalent residues and short description of the matched structure. List is sorted by RMSD, but this can be changed.
2.2. Measure(s) for goodness-of-fit and statistical significance?
Z score and P score
2.3. Structure-based sequence alignment?
yes, it contains both the secondary structure-based alignment and the 3D-structural alignment.
2.4. PDB files with superimposed structures?
No
2.5. Interface with visualization software?
No
2.6. Hyperlinks to the other web-based resources (e.g., PDB)
No

3.1. Are there parameters the user can set to optimise the results?
yes, one can choose lowest acceptible match between two structures.
3.2. Is there a choice of database? How much of the structural universe do they cover?
yes, one can choose between all PDB archive or SCOP 1.61
3.3. How often are the databases updated?
the same as PDB's frequency of update (once a week)