• P-ISSN 0974-6846 E-ISSN 0974-5645

Indian Journal of Science and Technology


Indian Journal of Science and Technology

Year: 2021, Volume: 14, Issue: 16, Pages: 1296-1301

Original Article

PDBcle – An online tool for extracting chain structure and sequence of macromolecule and small molecule structure from the Protein Data Bank

Received Date:14 February 2021, Accepted Date:02 May 2021, Published Date:10 May 2021


Background: Protein Data Bank (PDB) is the most popular structure database that contains experimentally determined three-dimensional (3D) structures of biological macromolecules and small molecules. The rich features of PDB are keyword assisted advanced text search, structure search by sequence alignment, sequence motif search, ligand to target-ligand complex search through SMILES substructure search, JSON API query search, structure alignment, structure quality assessment, genome viewer, and 3D structure viewer. It is widely used in molecular modelling and computer-aided drug design. PDBcle is a simple tool to extract chain sequence of protein/nucleotide and 3D structure of protein/ nucleotide/ ligand from the PDB. Objectives: To construct an online tool for separating molecule-wise chain sequence and structure of polymers and non-polymer structures in a macromolecule. Moreover, the separated sequences and structures are produced to moleculespecific standard file format. Methods: The graphical web-interface of PDBcle tool has been designed using PHP, CSS, and pure JavaScript. Parsing the atomic coordinate records and sequence records from the PDBML/XML file and/or PDBx/mmJSON file through the API of PDB was done through PHP server script. Findings: The PDBcle tool retrieves and generates separate structure/sequence files for each amino acid/RNA chain, and pair of chains for DNA base pairs with/without ligand complex from the PDB. The ligand molecules are separated and sorted from the chains and produced to an SDF file. Applications: PDBcle tool is publicly accessible at https://www.biogem.org/tool/pdbcle/.

Keywords: PDBcle; PDB; PDB Chain and Ligand Extractor; PDB Sequence Extractor; PDBML


  1. Berman HM. The Protein Data Bank. Nucleic Acids Research. 2000;28(1):235–242. Available from: https://dx.doi.org/10.1093/nar/28.1.235
  2. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR. The protein data bank: A computer-based archival file for macromolecular structures. Journal of Molecular Biology. 1977;112(3):535–542. Available from: https://dx.doi.org/10.1016/s0022-2836(77)80200-3
  3. Bourne PE, Berman HM, Mcmahon B, Watenpaugh KD, Westbrook JD, Fitzgerald P. Macromolecular Crystallographic Information File. Methods in Enzymology. 1997;277:571–590. Available from: https://doi.org/10.1016/S0076-6879(97)77032-0
  4. Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM. PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics. 2005;21(7):988–992. Available from: https://dx.doi.org/10.1093/bioinformatics/bti082


© 2021 Ashok Kumar.This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Published By Indian Society for Education and Environment (iSee)


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