ProSAT2
Protein Structure Annotation Server
Please use our updated server at: http://prosat.h-its.org



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:
VARIANT and MUTAGEN key feature from UniProt Knowledgebase
Mutation information from BRENDA

(2) from user-supplied annotations:
Rendering user-supplied annotations

References

Some usage examples



To display
VARIANT and MUTAGEN key feature from UniProt Knowledgebase :

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)

SwissProt entry ID/accession code or an EC number:
PDB id(s) :


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.

Enter 4 number EC code:
PDB id(s):

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 (local) filename with annotations (format requirements here):

The (local) filename of your protein 3D structure :


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).



References:

ProSAT2 homepage address:
http://projects.villa-bosch.de/mcm/database/prosat2/

R.R. Gabdoulline, S. Ulbrich, S. Richter, R.C. Wade
ProSAT2 - Protein Structure Annotation Server
Submitted

R.R. Gabdoulline, R. Hoffmann, F. Leitner and R.C. Wade,
ProSAT: functional annotation of protein 3D structures
Bioinformatics (2003), 19, 1723-1725


R.R. Gabdoulline,
S. Ulbrich,
S. Richter,
R.C. Wade
02.2006, R.Gabdoulline