PDBms-An online tool for PDB file splitting and interactive molecular visualization

Interdiscip Sci. 2023 Mar;15(1):146-153. doi: 10.1007/s12539-022-00539-7. Epub 2022 Sep 30.

Abstract

The rapid growth of biological databases has resulted in the vast development of many state-of-the-art molecular analysis tools for accurate disease diagnosis and drug discovery. Protein Data Bank (PDB) is a leading molecular database consisting of three-dimensional (3D) experimental structures of macromolecules and small molecules. The most significant role of PDB in Bioinformatics includes molecular modelling and computer-aided drug design (CADD). PDBms is a web tool for splitting PDB file and interactive visualization of molecules. It parses coordinate section records in the PDB file and categorizes them into a group of molecules. Moreover, it supports 3D graphic visualization in the various model for polymers and target-ligand interactions of complex structures. The web interface of PDBms is designed using NGL Viewer/WebGL JavaScript package and programming languages such as PHP, HTML, CSS, JavaScript, AJAX, and jQuery. PDBms is freely accessible at https://www.biogem.org/tool/pdbms/ .

Keywords: PDB; PDB File Parser; PDB Splitter; PDBms; RCSB PDB; wwPDB.

MeSH terms

  • Databases, Protein
  • Drug Design*
  • Drug Discovery*
  • Internet
  • Macromolecular Substances / chemistry
  • Protein Conformation
  • Software

Substances

  • Macromolecular Substances