Functionality test -Combinatorial Extension

You can find the server here

1.1. User interface, on-line help, choice of parameters and databases
very transparent, hyperlinks to starting page, help page and references. On the starting page you have to choose(upload) file, choose database to search in and type your email address.
1.2.Interactive versus E-mail results or notification
upload interactive, results also interactive, but the finish of the process is announced by email(it is compulsory and not optional as is mentioned on the page).
Upload on NT machine doesn't seems to work, only from Unix operation system.
1.3. Documentation, access to literature references
functional hyperlink to pdf. version of original method describing paper and to some other pdf version of papers with results, when the method was used.
1.4. Confidentality
I haven't found any information.
1.5. Elapsed time between submission and results
5 min to 15 min (but eventually also 20 hours)
1.6. How long are the results kept on the server ?
At least two days

2.1. What information is reported for the hits?
For each of the hits contain PDB id, z score, rmsd, number of identical residues, experimental method used for structure determination, size of gap (if any) and short description of matched structure.
2.2. Measure(s) for goodness-of-fit and statistical significance?
reports all structures with Z-score higher than 3,7. Z score is is relevance compared to results with random sequences
2.3. Structure-based sequence alignment?
yes, very well accessible and transparent
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)
Links to PDB

3.1. Are there parameters the user can set to optimise the results?
you can specify selection criteria only for know structures (z-score, RMSD, gap length, length difference) !
3.2. Is there a choice of database? How much of the structural universe do they cover?
between PDB and representatives of PDB
parameters for generating representatives:
- The RMSD between two chains is less than 2A.
- The length difference between two chains is less than 10%.
- The number of gap positions in alignment between two chains is less than 20% of aligned residue positions.
- at least 2/3 of residue positions in represented chain are aligned with representing chain.
3.3. How often are the databases updated?
no information, but probably as often as PDB (once a week)