SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 6

1.2.3 Web Interface

From the user point of view, the use of SuMo involves several steps:

1.2.3.1 Choice of a Target Structure

First step, the user has to specify a 3D protein structure as target. This target can be
either a file to upload or a PDB id. A selection within this structure can be performed.
The user can select either the whole protein or only some chains or some sites bound
to ligands. From this selection, SuMo will give the list of retained chemical groups.
A non-interactive interface using a simple query language (SuMoQ) is also proposed
to advanced users to allow more flexibility in the queries.

1.2.3.2 Choice of SuMo Database

The second step is to select the database to scan. A first database available consists
of all the PDB structures in which only redundant chains (sharing 100% sequence
identity) have been removed. The second database consists of the ligand binding
sites that are found in the PDB database. In order to keep a large panel of conforma-
tional variants of the proteins, the variety of structures of proteins of identical or
very close sequences is preserved. Selection can contain either the full list of struc-
tures in the database or just a subset.

1.2.3.3 Presentation of Results

After comparing the selected target against the previously chosen database, results
are displayed in a table as a list of potentially interesting similarities (Fig. 1.2 ).
Results can be sorted according to different criteria, such as the volume of the
matched sites, the number of matched pairs of chemical groups, the number of
amino acids involved or the SuMo score. The query specification and the results can
be saved or exported as text for further analysis.
In the case of scanning the database of ligand binding sites, results are also sum-
marized as a mapping of the potential ligand binding chemical groups in the query
structure and as a list of potential ligands sorted by maximal score (volume of the site).
Links to the PDBSum web site are also available for complementary informations.

1.2.3.4 Detailed Results

For each pair of matched 3D sites, detailed information is given (Fig. 1.3 ): description
of the chemical groups that matched, parallel view of both sites in the same orientation,
direct view in RasMol, links to other resources. Also, various numerical parameters
are given as a support for extended analyses of the results.