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

T Ashok Kumar

doi:10.17485/ijst/v14i16.282

Abstract

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

Highlights

Theoretical and computational molecular modelling are the most promising approaches used in Computer-Aided Drug Design (CADD) to reduce the experimental costs and duration
Protein Data Bank Markup Language (PDBML) is a document markup language defined by Protein Data Bank (PDB) that consist of a set of Document Type Definition (DTD) framed according to SGML protocol
Each PDBML/eXtensible Markup Language (XML) files consist of different schema referenced by the PDB exchange data object for atomic coordinates [5]

Summary

Introduction

Theoretical and computational molecular modelling are the most promising approaches used in CADD to reduce the experimental costs and duration. 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. 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.

Objectives

Methods

Results