Dali

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 easy to use, just download the structure if you have new versions of browser (bigger than Explorer 5.x and Netscape 4.5), otherwise email submission; no other possible operation
1.2.Interactive versus E-mail results or notification
The results are delivered only in e-mail form
1.3. Documentation, access to literature references
on the main page there is a original paper describing the method and small old review(1994) about a structural comparison both in html format.
1.4. Confidentality
From the help page:
"Your coordinates and the search result are deposited in a directory to which only the Dali server administrators have read access. No one else inside or outside of EMBL-EBI can read your data, except our systems administrators who are held to the highest standards of confidentiality.
The PDB identifier of the best hit plus your name and address is archived in a protected directory. All other data is deleted immediately after completion of a request."
1.5. Elapsed time between submission and results
Usually very fast (4-8 minutes), but eventually can be slow and take a few hours (either due to high server load or it can not match precalculated results ).
1.6. How long are the results kept on the server ?
They are not kept at all, the results are sent through email.

2.1. What information is reported for the hits?
It contains PDB ID of similar structure, z score, RMSD, number of equivalent residues and others. List is sorted by z-score. Presentation dependent on a used email program.
2.2. Measure(s) for goodness-of-fit and statistical significance?
Z score- strength of structural similarity in standart deviation above expected
2.3. Structure-based sequence alignment?
yes, structural alignment in text format (list of equivalent fragments between structure), not very friendly (very tough to find needy information)
2.4. PDB files with superimposed structures?
Not directly
2.5. Interface with visualization software?
No.
2.6. Hyperlinks to the other web-based resources (e.g., PDB)
link to FSSP database (from results) and to FSSP and Dali domain dictionary and MaxSprout (reconstruction of full coordinates from C-alpha trace) from main page.

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?
no, it searches in the subset of PDB (contains structures with sequence identity less than 25 percent), but it is not easy to gain this information, only if you submit structure by email you can meet this information
3.3. How often are the databases updated?
the same as PDB's frequency of update (once a week)