ProSAT2 is a server to select and group residue based annotations and explore
them interactively on a 3D structure of a protein. ProSAT2 includes features of
ProSAT version 1
(Protein Structure Annotation Tool) for displaying SwissProt and ProSite annotations.
The residue-based information may be extracted from databases (e.g.
BRENDA or UniProt) or user defined. Visualisation is based on the
WebMol,
Java Protein viewer. See example snapshots from ProSAT2 sessions below.
(click images to enlarge)
The Java plugin version 1.5 or higher is needed for visualisations.
To display residue specific information :
(1) from databases:
Enter SwissProt ID/accession code or EC number of an enzyme and related pdb ID
(for example, ANT3_HUMAN and 1att for antitrypsin or 3.2.1.17 and 1cj6 for lysozyme)
VARIANT and MUTAGEN information will be parsed and mapped to the PDB structures, visualisation will be
provided via a Java applet. Instructions, how to use the visualisation tool, can
be found here
During visualisation you can define new groups of residues; save the
modified annotation file (cut'n'paste) for later visualisations using
"User-supplied annotation" form below.
In the case when one of the fields is left empty, the server will
search for missing data and prompt you to choose relevant information (may take some time).
To display information from the engineering section in
BRENDA on a protein structure:
Enter a 4 number EC code and related pdb ID(s) (for example, 3.8.1.5 and
1hde for Haloalkane dehalogenase). If no pdb ID is entered, ProSAT2 will use
all structures referenced in the BRENDA entry.
Mutation information will be parsed, PDB files will be downloaded, mutations and
ProSAT
version 1 annotations will be mapped to the
PDB structures, visualisation will be
provided via a Java applet. Instructions on how to use the visualisation tool can
be found here .
If no sequence is available in the BRENDA page for the protein for
which the mutations are reported, then the parser will not be able to
map the mutation to the structure(s).
During visualisation you can define new groups of residues; save the
modified annotation file (cut'n'paste) for later visualisations using
"User-supplied annotation" form below.
To render user-supplied annotations:
Enter the names of the annotation file
and the pdb file to map these
annotations to:
The use of only one pdb file is supported currently;
the first pdb id from the xml page will be taken if more than one is specified.
Here are examples of pdb and annotation files (these can be
saved locally and submitted to the server).
