Pages for each target in the TDI Kernel database are divided in three main sections.

• Target general data
• Binding site predictions
• Communication tools

This section of the page shows the name of the target and the MSDChem ids for predicted ligands by AnnoLyze, followed by a link to the UniProt page of the target as well as the organims of the gene.
The second line show selected keywords related to the target and predicted ligands.
Finally, a rating system allows registered users to rate the target for its potentiality for drug discovery against tropical diseases. The rating system ranges from 0 to 5 stars, where 5 stars means greater potentiality than 0 stars.

Each prediction by the AnnoLyze method of a ligand binding to a model build by using the MODELLER program is shown in a single row. Each row shows the basic data for understanding the accuracy of the prediction, which are:

• - A “+” sign shown if more than two ligands are predicted. By clicking in the “+” sign more data about the prediction is shown (see below).
• - PDB: Identifier for the original protein co-crystallized with the predicted ligand.
• - Expansion values (see the methods page for more info on expanding a ligand binding site). The numerical values indicate the % of sequence identity and coverage of the binding site after optinal structural alignment of the binding site protein and the template used for modeling.
• - Template: Identifier for the structure used for modeling the 3D structure of the target.
• - Modeling values (see the methods page for more info on model building). The numerical values indicate the % of sequence identity and the ModPipe Quality Score (MPQS) of the model. A MPQS higher than 1.1 predicts correct models.
• - Model: Identifier for the 3D predicted structure of the target.
• - Inheritance values (see the methods page for more info on inheriting a ligand binding site). The numerical values indicate the % of sequence identity and coverage of the binding site bsed on the sequence alignment between the template and the traget structure used for model building.
• - Ligand: PDB id for the inherited ligand.
• - Exact: Exact tanimoto match between the smiles of the inherited ligand and a drug deposited in the DrugBank database.
• - SupStr: Supra-structure tanimoto between the smiles of the inherited ligand and a drug deposited in the DrugBank database.
• - SubStr: Sub-structure tanimoto match between the smiles of the inherited ligand and a drug deposited in the DrugBank database.
• - Similar: >=95% tanimoto match between the smiles of the inherited ligand and a drug deposited in the DrugBank database.

If more than one ligand is predicted to bind the 3D model of the target, the details on the predictions are hidden. The user can see the details by clicking on the “+” sign at the beginning of the row. Next image shows the details of target A5K6S2 predicted to bind MOA (MYCOPHENOLIC ACID).

The structural superimposition of the MOA ligand with its original PDB, the template and the target model is shown in the inner image. By clicking into the image, the user can download the coordinates of the superimpostion. Details such as structure, drug name, drug category, drug type and drug indication for each exact, supra-structure, sub-structure or similar drugs to MOA are also shown. Please, note that no actual ab-initio docking was peformed on the models and that the superposed coordinates correspond to the original orientation of the ligand. For more information read the methods page.

This section of the allows users to bookmark the current page to several social networks. Moreover, registered users can leave written comments about the target.
If a user is also registerd with our partner The Synaptic Leap (TSL) can directly blog in TSL about this particular entry by clicking to the “TSL BLOG IT!” button in the sidebar of the page.

The sidebar also shows a search box, links to our static pages for browsing, downloading, help and methods descriptions. Additionally,a summary of the highest rated targets for drug discovery.