You can find the server here
very simple, not so many possibilities - only file window, email address (optional), choice of database and choice between core and pre-core superposition
upload and also results interactive, you can get e-mail message about finishing the process of searching. You can not load directly the saved file, you have to copy whole .pdb file to the window or you can use PDB ID (but new structures don't have ID).
Original paper in the .pdf format on the page
No information
it depends on chosen parameters and length of query structure,(pre-core superposition with smaller database and shorter protein is more rapid). It is among 5 and 45 minutes
Authors announce 6 hours, but I was able to get back result even 4 days after the search
contains list of matched structures sorted according to number of matched residues. To each matched structure, there is information about RMSD for matched residues and structural alignment in three forms (text, PDB and Chime) and pdb header
number of matched residues and RMSD for them
yes, in three forms and even text form is very good and useful (PDB and Chime format are the others).
yes, if you have Rasmol or Chime
links to Rasmol and Chime
you can choose between pre-core and core superposition, pre-core is quicker and should not be able to distinguish so well biologically meaningful and meaningless results.
One can choose between six subsets of PDB generated by program Obstruct
Heringa J, Sommerfeldt H, Higgins D, Argos P. (1992). OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput Appl Biosci 8(6):599-600
| Max. Homology | Resolution (A) | Number of proteins |
| 25% | 1,8 | 201 |
| 40% | 1,8 | 244 |
| 25% | 2,0 | 312 |
| 40% | 2,0 | 388 |
| 25% | 2,5 | 474 |
| 40% | 2,5 | 582 |
I was not able to find more information about subsets, but I guess from the size of databases, that the subsets are not updated at all since 1997
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