APDB: Database of Air Pollutants

Documentation

 

APDB: a database on air pollutants characterization and similarity prediction

APDB is an essential resource which improves our knowledge on the existing air pollutants, their molecular properties and mechanisms of action. This database contains a collection of pollutant molecules mainly from online resources provided by the Environmental Protection Agency (EPA):

In APDB, air pollutants are chemically annotated and their activity in relation to the inhibition or activation of specific protein targets is reported. Annotation is accomplished through PubChem identifiers such as PubChem Compound Identification (CID), CAS, InChIKey, canonical SMILES and molecular formula. Activity is retrieved by listing associated targets and bioassays found in the PubChem BioAssay repository. Molecules are characterized through molecular fingerprints and descriptors calculated with PaDEL-Descriptor software and quantum-mechanical properties computed with the quantum chemistry program Jaguar. Similar molecules are derived from molecular descriptors and properties by applying the most common similarity measures after accurate data preprocessing.

  

Home Page
Through the Home section, users can browse molecules, targets and bioassays, descriptors, and similarities by clicking on the corresponding "Run" button.
Molecules List
The molecular annotation card leads to the list of molecules. Molecules are specified by the following identifiers:
  • Chemical Name
  • CID
  • CAS
  • InChIKey
  • Canonical SMILES
  • Molecular Formula
Molecule atoms can be filtered by clicking on an element from the periodic table. By pressing the download button at the bottom of the panel, users can obtain a CSV file with the entire table or with the selected items from the column checkboxes, the periodic table, or the search form. Molecules can be searched by all their identifiers. In the first form, the user can specify the type of identifier and in the second form, can select the desired entry. By clicking on a CID entry, users are redirected to the similar molecules panel.
Biossays List
The targets & bioassays card leads to the list of biossays. Bioassays are specified through the assay ID (AID), associated CID, activity value in µm, activity name, assay name, assay type, and PubMed ID. Targets are inserted by their:
  • GenInfo Identifier (GI)
  • Gene ID
  • Symbol
  • UniProtKB
By pressing the download button, users can obtain a CSV file with the whole table or with the selected items from the column checkboxes or the search form. In the first form, the user can specify the type of target identifier type and in the second form, can select the desired entry. By clicking on a UniProtKB entry, users are redirected to the target panel containing additional information on the searched target.
Target Panel
In the selected target panel, users can visualize the optimized PDB structure generated with 3Dmol.js and download the file via the “PDB” button. If the PDB structure is not available, users can download and explore the predicted protein structure on the AlphaFold page. Molecules associated with the searched target can be downloaded as a CSV file by pressing on the download icon in the table header. By clicking on a CID entry, users are redirected to the similar molecules panel.
Descriptors Panel
Fingerprints are illustrated through an interactive radar chart representing the distribution of the inverse-document-frequency weights, while molecular descriptors and quantum properties are illustrated through a scatter plot matrix. By pressing on the download icon, users can obtain a CSV file with the desired descriptor table.
Similarities Search
Similarity spaces are illustrated through an interactive scatter plot of k-means clusters projected to 3D with t-SNE. A legend shows for each cluster the number of similar molecules found. By pressing on the download icon, users can obtain a .zip file with the corresponding embedding model from Node2Vec (note that molecular descriptors and quantum properties also include the model for single elements). Similar molecules can be retrieved by inserting the CID or InChIKey of a molecule of interest in the search area.
Similarities Panel
The similarity panel of a query molecule shows molecular info together with the 2D structure generated with RDKit and the list of similar molecules ranked by the number of intersecting chemical spaces (indicated with different colours) and the average similarity computed across spaces. Users can change the similarity threshold in the range of 0.75-0.99 (default is 0.95); if no similar molecules are found, those with the closest threshold are returned. The “SDF” button allows downloading the optimized SDF file for the searched molecule. Similar molecules can be downloaded as a CSV file by pressing on the download icon in the table header.
 

License

Copyright (c) 2023 by Eva Viesi | InfOmics

Except where otherwise noted, this website and all its content is licensed under a MIT License.