You can find the server here
On the first page there is a choice of different databases to search in, each database has its own page. If you proceed directly to page with your database of choice you can skip to page with more control (control of parameters settings and output settings).
submitting interactive, results by email ( plus contain hyperlink to a web page where the results are keep alive).
there is a hyperlink reference to paper describing the method, clicking on the hyperlink goes directly to .pdf format of the article, but it does not work, the article does not appear on the screen. There is also description of the parameters and other things on main page
No information
Faster with SCOP database than with PDB database, but still very divergent: 5minutes to two hours (usually about 20 minutes)
Results go both to mail are kept on web page for three days (hyperlink in the mail)
two parts: first part is complete list of hits with structural alignments and PDB headers to matched structures - pretty useless, because of the length (1050 pages for 1cbs structure), the second part is brief summary table with SCOP and PDB codes to matched structures (and hyperlinks to them in these databases) and information about structural diversity, number of matched residues, topological diversity and number of matched SSE. This is clear and useful
two parts: first part is complete list of hits with structural alignments and PDB headers to matched structures - pretty useless, because of the length (1050 pages for 1cbs structure), the second part is brief summary table with SCOP and PDB codes to matched structures (and hyperlinks to them in these databases) and information about structural diversity, number of matched residues, topological diversity and number of matched SSE. This is clear and useful
yes, in text form, very difficult to use, because it is sheltered from you in 1050 pages of the results (for 1cbs).
No
No
to SCOP (did not work), to PDB atlas
You can change almost everything: residue number of a shortest fragment, shortest distance between a pair of aligned Ca atoms, allowed RMS of representing points for a helices and b strands, allowed angle of direction difference for a helices and b strands and finally allowed line to line distance for a helices and b strands
between SCOP, entire PDB and in PDB atlas with possibility to reduce search with keywords. In the Scop database, you can choose between four different subset :
No information about this server,Scop approximately twice a year, PDB once a week
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