PDB@: An offline toolkit for exploration and analysis of PDB files

Abstract

Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

Unraveling the Molecular Mechanism of Xuebijing Injection in the Treatment of Chronic Obstructive Pulmonary Disease by Combining Network Pharmacology and Affymetrix Array

“…Molecular docking was performed using AutoDockTool 1.5.6 and Auto Dock vina to verify the binding activity of the active compound of XBJ to the core target protein. The 3D structures of the compounds were available in the PubChem database, and the core target proteins were accessible in the PDB database 27 (https://www.rcsb.org/). The screening criteria for the target proteins were (1) The organism was Homo sapiens .…”