The BioSight platform is an online web service that offers an integrated access to all applications developed by the Bionext company. For the times being the only application made accessible through BioSight is Target Analysis. Others are under development and will be added later.
The Target Analysis service of the BioSight platform
Target Analysis is dedicated to the retrieval of common patterns at the surface of macromolecules. Based on a user defined query pattern, Target Analysis iterates over a large database of structures and identifies at the surface of these macromolecules areas that are similar to the query.
Key elements of a Target Analysis analysis
- The query pattern: Although theoretically any selection of surface atoms could be used as a query pattern for a Target Analysis, Biosight restricts the selection of query patterns to “interaction sites”, e.g. areas of a macromolecule under a certain threshold distance of another macromolecule or of a ligand present in the same structure. Select a macromolecule, an interactant and let BioSight define the query site for you. Although this should be enough for most applications, workarounds exist for finer tuning of the query pattern.
- The Target Analysis database of structures: Bionext default database for Target Analysis comprises all macromolecular chains that can be found in the PDB. It is updated every month and subsets are also provided based for instance on organisms, or to avoid protein redundancy. Insertion of in-house structures in the database is not possible in the on-line version, but is possible for on-site installation of the BioSight platform.
- Key features of Target Analysis results: On each structure of the database, Target Analysis identifies sites that are similar to the query. These so called target sites are superimposed on the query site and a similarity score is attributed to the superimposition. Target sites for all structures of the database are then gathered and ranked according to their similarity scores. Through BioSight you will be able to access this ranked list and visualize the superimposition of each predicted target site on the query site. Moreover, for each superimposition it is possible to display a color coded set of rods connecting similar atoms in the two structures. This allows for grasping the nature of site similarity in the blink of an eye.
Explore yourself BioSight capabilities: showcases
Several showcases are freely accessible once registered at biosight.bionext.com, with the complete results you would obtain for these chosen queries. The Target Analysis is able to top rank several proteins (out of > 35,000), with totally different folds, but sharing the same or similar ligands.
Here is an extract of the most outstanding results:
- Muscarinic receptor M2 (GPCR class): found Dopamine transporter at rank 6;
- Neurotransmitter symporter (Transporter class): found Muscarinic receptor M3 at rank 61;
- DHODH (Enzyme from pyrimidine pathway): found Molybdenum storage protein at rank 14, with substrates similarity;
- MAPK12 (Kinase class): found Synapsin at rank 92 (1st non-kinase protein in these results);
- Trypsin (Protease class): found Subtilisin at rank 63.