Matras

You can find the server here
You can start your search directly here

1.1. User interface, on-line help, choice of parameters and databases
very simple, email address field, upload field and database choice
1.2.Interactive versus E-mail results or notification
upload interactively, results by email. It enables to choose the particular part of interest of PDB file (define the range), because it doesn't handle multidomain protein
1.3. Documentation, access to literature references
hyperlink reference to original paper abstract at Pubmed
1.4. Confidentality
I haven't found any information
1.5. Elapsed time between submission and results
usually to twenty minutes, It seems to be very dependent on the length of protein
1.6. How long are the results kept on the server ?
email results only

2.1. What information is reported for the hits?
"Dali like format": rank, PDB ID, R- distance, Z-score, seq. identity measure and name of the molecule from PDB header
2.2. Measure(s) for goodness-of-fit and statistical significance?
Z-score (show all results with Z-score higher than 4)
2.3. Structure-based sequence alignment?
yes, very difficult to use. Structural alignments cover second, larger part output file. There are no hyperlinks to structural alignment from matched structures, therefore is very difficult to find the alignment in long list of results.
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?
No
3.2. Is there a choice of database? How much of the structural universe do they cover?
yes, between 40 % representatives of PDB(default) and 40% representatives of Scop database
3.3. How often are the databases updated?
once a week in the case of PDB and twice a year in the case of SCOP