PDBms

PDBms parses and categorizes Protein Data Bank (PDB) files and renders interactive 3D molecular visualizations to support molecular modeling and computer-aided drug design (CADD).

Key Features:

• PDB file splitting: Parses the coordinate section records within a PDB file and categorizes them into distinct groups based on molecule types.
• Interactive 3D visualization: Renders 3D graphics of polymers and target–ligand interactions to inspect structural relationships within complexes.
• Computational stack for rendering: Uses NGL Viewer/WebGL for 3D rendering and is implemented with PHP, HTML, CSS, JavaScript, AJAX, and jQuery.

Scientific Applications:

• Molecular modeling: Enables inspection and decomposition of macromolecular structures for modeling tasks.
• Computer-aided drug design (CADD): Supports detailed examination of drug–target interactions relevant to drug discovery.
• Structural biology and protein engineering: Facilitates targeted analysis of specific components within complex structures for structural studies and engineering efforts.

Methodology:

Parsing of PDB coordinate section records, categorization of entries by molecule type, and rendering of interactive 3D models using NGL Viewer/WebGL; implementation components include PHP, HTML, CSS, JavaScript, AJAX, and jQuery.