Examples of PungentDB usage are provided below. A movie illustrating each special example was recorded from the PungentDB website; the movies can be accessed from the ‘Examples’ link of the PungentDB.
Searching for pungent molecules structurally similar to a compound satisfying Lipinski’s rule of five. This rule is based on properties of known orally available drugs. It states that, an orally active drug has no more than one violation of the following criteria: No more than five hydrogen bond donors; No more than 10 hydrogen bond acceptors; Molecular mass less than 500 Da; an octanol–water artition coefficient (log P) not >5. Moreover, one can also search the ligands of special TRPs or ORs family receptors from these pungent flavor compounds in the sections of ‘Identifiers’ and TRPs or ORs receptors section.
Zingerone (COc1cc(CCC(C)=O)ccc1O, PID00058) is one of pungent molecules present in pungent flavour TCMs: Zingiberis Rhizoma (Gan Jiang in Chinese name) , Alpiniae Officinarum Rhizoma (Gao Liang Jiang in Chinese name), Zingiber Rhizoma Recens (Sheng Jiang in Chinese name), Rhizoma Zingiberis Praeparata (Pao Jiang in Chinese name). Its flavour profile is strong Pungent Odor Reminiscent of Ginger, Sweet, Spicy Taste. Using the structural similarity search, one can get a list of similar molecules in PungentDB. The top result for this example is Vanillin (PID00013) with 73.08% similarity, excluding Zingerone itself in PungentDB.
The PungentDB database provides an easy-to-use platform for users to browse, search, and analyze Pungent compounds related information from various aspects. One can browse all the pungent compounds and detailed information by click the name of pungent compounds. Each pungent compound has 9 sections to describe specific information. The ‘Pungent TCM’ page provides the list of these pungent TCMs related pungent compounds. At last, one can browse the dynamic network of Pungent TCM-compound-target (TRPs and ORs) by clicking the ‘View TCM-C-T network’ links.
PungentDB provides 61 TRPs family protein structure with three type visual tools, including NGL(webGL), 3Dmol, LiteMol. One can choose a viewer from the ‘Select a different viewer’ drop-down tab as the 3D visualization tool to display the protein structure on your browser. Additionally, you can also choose one protein from the ‘Select Receptors’ drop-down tab to display its structure from the ‘Select Receptors’ drop-down tab.
We created a custom database of protein sequences associated temperature and odor. The Alignment contains the 71 TRPs receptors (Human and other species) and 33 olfactory receptors (Human and other species), they are displayed with bioJS MSA. The Basic Local Alignment Search Tool (BLAST) alignment was generated using the PROMALS3D webserver. The user is able to control the different setting parameters to display difference style visualization for the protein sequence.
Pungent ViroBLAST is a stand-alone BLAST web interface for TCM nucleotide and amino acid sequence similarity searches and it contains 36 TCMs genomic datasets. It extends the utility of BLAST to query against multiple sequence databases and user sequence datasets, and provides a friendly output to easily parse and navigate BLAST results. Pungent ViroBLAST is readily useful for TCMs research areas that require BLAST functions. One can upload query sequence file in FASTA format or enter query sequences into input box, and then you can also choose program and select one or multiple databases. One can set the optional search features for advanced users who need to glean more specific information in the ‘Advanced Search’ section.