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MED-SuMo GUI 1.1.38 screenshots and features


Connect to the server

 

 

Fig.1: The configuration window enables the connection to the MED-SuMo server. The IP address and port number are required to connect to the server. A profile corresponding to MED-SuMo databases and a login/passwd is defined for each user. A drop down menu helps to select the precomputed MED-SuMo databases available on the server. The profile needs to be defined for each user by the administrator with the MED-Manager. Databases are either sites database (e.g. db45) or full database (dbfull). db45 stands for a database of sites defined by the 4.5 Å environnement of the ligand. Others databases are computed  with different triplets parameters (e.g. 13-39 or 20-60).

 

Build the query

 

The query is a surface of a protein (locally stored or from the database). The surface is described by a graph of triplets of surface chemical features.

 

Depth Cueing

 

 

Fig.2: Graphical representation of a query: protein (cartoon, blue) ; ligand (stick, carbon atoms grey) ; MED-SuMo Surface Chemical Features (balls and sticks). A few chemical features are labeled with the associated residue (e.g. ARG 221) and their type (e.g. guanidinium). The miniview window helps to set graphically the depth cueing.

 

Visualize the triplets of surface chemical features

 

 

Fig.3: Graphical representation of a query: protein (cartoon, blue) ; ligand (stick, carbon atoms grey) ; MED-SuMo Surface Chemical Features (balls and sticks). A few chemical features are labeled with the associated residue (e.g. ARG 221) and their type (e.g. guanidinium). The SuMo Objects window helps to visualize the query as it is processed by MED-SuMo heuristic (e.g. a graph of triplets of Surface Chemical Features). By clicking on one object (hydrophobic Phe 182), all the triplets containing this object are shown in the 3D viewer as semi-transparent light blue triangles.

 

Use the treeview to choose residues or atoms to define the query or change the rendering

 

 

Fig.4: Graphical representation of a query: protein (lines, carbon atoms grey) ; ligand (stick, carbon atoms grey) ; MED-SuMo Surface Chemical Features (balls and sticks). A few chemical features are labeled with the associated residue (e.g. ARG 221) and their type (e.g. guanidinium). The treeview window helps to select residues, atoms in the viewer and to manually define the query or change the rendering.

 

Choose the query: autodected site

 

 

Fig.5: Graphical representation of a query: protein (lines, carbon atoms grey) ; ligand (stick, carbon atoms grey) ; MED-SuMo Surface Chemical Features (balls and sticks). A few chemical features are labeled with the associated residue (e.g. ARG 221) and their type (e.g. guanidinium). The query window Tab\  Reference Protein helps to choose the definition of the query. Here, an autodected binding site is selected. Autodetected binding sites are due to the presence of a co-cristallized ligand, heteroatoms or small peptide (by default less that 10 residues).

 

Choose the query: user defined advanced query

 

 

Fig.6: Query window / Tab Reference Protein showing the advanced mode. A query can be defined by a logical combination of rules. The rules are stated as (around or equal) from (residue, atom, atoms, object, object type, residu type, manual query). Here an example is shown where all the objects of the proteins are selected (full surface) except the environement of the ligand IZ3.

 

Choose the database

The MED-SuMo databases (Sites or Full) are precomputed. The user chooses the database at the moment of the connection >>. Before launching the job, the user can select a subset of the database or compare the query to a single file stored locally).

Database explorer

 


 

Fig.7: Database explorer window helps to make a subset selection from the structure database. Here the PDB is parsed with the keyword phosphatase. Other fields that can be queried are shown in the drop down menu. Using a subset helps to focus on a given family, on X-ray structure with a minimal chosen resolution or from a given author... The list of PDB codes can be saved as a file with the extension .sub. It can be used in Query window to launch a run on a subset of the database.

 

Choose the structures of the database: whole database, subset only, a single locally stored structure

 

 

Fig.8: the Query window / Tab Compare To helps to choose if a database is used or a single structure (which could be stored locally). A subset of the database can be chosen putting the names in the window (e.g. 4 letters code for PDB files), this subset can be built with the database explorer.

 

Browse the results

 

the result table

 

Fig.9: the Result window is a spreadsheet containing the hits. The hits are sorted by default with a decreasing MED-SuMo score order. The most important columns are shown: hit number, hit ligand 2D depiction, checkboxes to superpose the hits (protein and ligand) to the query in the 3D viewer window, the PDB code, the PDB ligand code, the MED-SuMo score, the signature of 3D chemical features. The MED-SuMo site database contains both synthetic ligand, peptides and peptidomimetics.

 

View  hits superposed to the query in the 3D viewer

 

Fig.10: The 3D viewer window helps to visualize the superpositions in 3D based on the superposition of the Surface Chemical Features. A hit protein (orange) is superposed to the query (grey), the ligands are shown with carbon atoms colored with the same colors. Surface chemical features are shown, they match by pairs.

 

Sort and select results

 

 

Fig.10: The Row Selection Window helps to select hits. Here a rule is created to keep only hits with a minimal MED-SuMo score of 4. Others rules can be added and a logical expression can be used.

 

Selected hits can be clustered according to their signature

 

 

Fig.11: The dendrogram window helps to choose the number of clusters by moving a slide bar. The signature consensus cutoff can be set. It corresponds to the percentage of occurences of a given feature in the consensus signature.

 

View results clustered according to their signature


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