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PDBSWS - REST access

Interrogate the mapping from your scripts

31.01.20 REST Access

The URI for REST access has changed (again!) The URI is now:

http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr

You may access the mapping directly from your scripts using a URI of the form:
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr

The fields in the URI are as follows:

FieldMeaning
plain=1This causes the CGI script to generate plain parsable text rather than HTML
plain=2This causes the CGI script to generate JSON output rather than HTML
all=yesThis causes a full alignment to be printed
qtype=tttttt is the query type which may be pdb, ac, or id
id=iiiiii is the PDB code, SwissProt identifier, or UniProt accession
chain=cccccc is the chain label used only when the query type is PDB
res=rrrrrr is the PDB residue identifier, or the residue number in the UniProt entry

For example:

      http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv&chain=y&res=24
      http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv
      http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv&all=yes
      http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=id&id=LYSC_CHICK
      http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=2&qtype=ac&id=P03952&res=400

Results

The results are returned in the form:

KeywordMeaning
PDB:PDB code
CHAIN:chain label
RESID:PDB residue id
PDBAA:Amino acid present in the PDB file
AC:UniProt accession
ID:UniProt identifier
UPCOUNT:Residue number in the UniProt sequence
UPAA:Amino acid present in the UniProt file
START:First residue in the PDB chain (if known)
STOP:Last residue in the PDB chain (if known)
ERROR:Error message (if any - database connectivity)

The RESID: PDBAA: UPCOUNT: and UPAA: fields will only be provided if a residue number has been used in the search.


Perl Modules

Two Perl modules are provided to make this easier from within your code


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