Topscan

You can find the server here

1.Operation

1.1. User interface, on-line help, choice of parameters and databases
only one page with very concise information about method and field for file load
1.2.Interactive versus E-mail results or notification
Both file load and results are interactive
1.3. Documentation, access to literature references
reference to the paper on the page
1.4. Confidentality
no information
1.5. Elapsed time between submission and results
very fast (no longer than one minute)
1.6. How long are the results kept on the server ?
Only until the window is active

2. Presentation of results

2.1. What information is reported for the hits?
very simple table with two column (one column with PDB ID of a matched structure and second with % score). I got 46 pages of the results(for 1cbs), because the database is redundantand and program provides a lot of structures as hits.
2.2. Measure(s) for goodness-of-fit and statistical significance?
% score. I haven't found any information, what it means.
2.3. Structure-based sequence alignment?
No
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)
yes, you can get to PDB sum

3. Implementation issues

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?
It uses PDB and you can choose between scoring against probe or against probe and database. But what is probe and what is database? What is the difference between them? Probe should be part of database, but how big part? Again without any presice information
3.3. How often are the databases updated?
No information, but probably as often as PDB

This is copy of warning from Topscan web page: TOPSCAN is a rapid method for comparing protein structures. It is useful as a preliminary screen to give you some idea whether your protein looks like something else. It trades coverage (and to some degree error rate) for great speed. If you want much more accurate comparisons you need to use a method which works at the detailed coordinate level such as SSAP.

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