About the PDTDB

Natural Medicine

PDTDB provides information about the phytochemical compounds, plant source for phytochemical compounds, drug targets, symptoms and causes of the diseases, and natural remedies to cure the diseases. Most of the data incorporated in this database were extracted from PDB, PubChem, and Wikipedia. The records in PDTDB are categorised into target and disease, plant, ligand, and docking. Hyperlinks in the database have tooltip text or thumbnail image or cross reference to the other records. The database consists of 3D structure of macromolecule and small molecule (target, ligand, and docking), amino acid sequence (target sequence in .fasta file format), and description (literatures reviews about target, disease, plant/herb, phytochemical, and docking). Users can access contents or retrieve files from PDTDB by text search, by browsing, or by batch download.

The database has been designed using PHP, MySQL, PDO, jQuery, AJAX, JSON, JavaScript, Dojo, HTML5, XML, and CSS3. Interaction of ligand-receptor complex is visualized using high graphics rendered 3D molecule visualization tool JSmol. Ligand search can be done using the Java chemical structure editor JSDraw.

The unique feature of PDTDB is the prediction of other plant/herb sources containing the identical phytochemical compound and phytochemicals involved in molecular docking, which leads to discover novel drug based on the existing molecular docking.