SSM v2.04

You can find the server here

1.1. User interface, on-line help, choice of parameters and databases
User-friendly. It allows to type a PDBID of a known structure, upload directly coordinates or even list of pairs. One migh choose lowest acceptible match or match connectivity or match individual chains.
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 author of the server answers the question readily and swiftly.
1.4. Confidentality
There is a link on the main pages to Privacy issues, where all the details are explained. The results are treated confidentially.
1.5. Elapsed time between submission and results
Usually very fast (in seconds), longest obserable time was 5 minutes (with the default parameters we used).
1.6. How long are the results kept on the server ?
Results expire in 4 hours.

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 Q-score, but this can be changed (by rmsd, align lenght, P-score, Z-score, matched SSE's.number of gaps, Sq %. It also gives rotational and translational matrices. It gives results in other formats as well (XML...) It is possible to download target or alignet sequences in FASTA format.
2.2. Measure(s) for goodness-of-fit and statistical significance?
Z-score, P-score and Q-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?
Yes, it doesn't give any limitation to number of superimposed structures.
2.5. Interface with visualization software?
Yes, RASMOL.
2.6. Hyperlinks to the other web-based resources (e.g., PDB)
Yes, long list - OCA,SCOP, FSSP, CATH, GeneCensus,3Dee, PDBsum, Swiss-Prot, ProtoMap, MSD Atlas

3.1. Are there parameters the user can set to optimise the results?
yes, one can choose lowest acceptible match between two structures or decide if you want to mach connectivuty or individual chains
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 1.63 pr SCOP 1.63 subset.
3.3. How often are the databases updated?
the same as PDB's frequency of update (once a week)