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

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 m...

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Bibliographic Details
Published inInterdisciplinary sciences : computational life sciences Vol. 15; no. 1; pp. 146 - 153
Main Author Ashok Kumar, T.
Format Journal Article
LanguageEnglish
Published Singapore Springer Nature Singapore 01.03.2023
Springer Nature B.V
Subjects
Bioinformatics
Biological effects
Biomedical and Life Sciences
CAD
Computational Biology/Bioinformatics
Computational Science and Engineering
Computer aided design
Computer Appl. in Life Sciences
Databases, Protein
Drug Design
Drug development
Drug Discovery
Health Sciences
Internet
Life Sciences
Macromolecular Substances - chemistry
Macromolecules
Mathematical and Computational Physics
Medicine
Molecular modelling
Original Research Article
Polymers
Protein Conformation
Software
Splitting
Statistics for Life Sciences
Theoretical
Theoretical and Computational Chemistry
Visualization
wwPDB
PDBms
RCSB PDB
PDB Splitter
PDB File Parser
PDB
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Summary: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/ . Graphical abstract
ISSN:1913-2751
1867-1462
DOI:10.1007/s12539-022-00539-7