PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Chemistry

Background:

• The Protein Data Bank (PDB) stores macromolecular structures in a machine-readable format.
• Interpreting PDB files requires specialized computational tools, limiting direct accessibility.
• Protein structures often exist with associated molecules like nucleic acids, ions, and drugs, all described in PDB format.

Purpose of the Study:

• To develop a free, web-based software tool for accessing and visualizing protein 3D structures from the PDB database.
• To transform PDB files into an easily understandable, human-readable format.
• To provide a comprehensive view of all information contained within a PDB file, including its 3D structure.

Main Methods:

• Development of a web application named PDB Explorer.
• Utilization of programming and scripting languages including Perl, CSS, JavaScript, Ajax, and HTML.
• Direct parsing of PDB files to extract secondary structure elements, atoms, and coordinates.

Main Results:

• PDB Explorer successfully converts PDB file data into readable sentences.
• The software displays comprehensive information from PDB files, including interactive 3D visualizations.
• The tool provides direct parsing of PDB file components such as secondary structures, atoms, and coordinates.

Conclusions:

• PDB Explorer offers a user-friendly interface for exploring protein 3D structures.
• The software democratizes access to structural biology data by simplifying PDB file interpretation.
• PDB Explorer is freely available online without requiring user login.