PDB explorer — A web based algorithm for protein annotation viewer and 3D visualization

• Published in: Interdisciplinary sciences : computational life sciences Vol. 6; no. 4; pp. 279 - 284
• Main Authors: Nayarisseri, Anuraj, Shardiwal, Rakesh Kumar, Yadav, Mukesh, Kanungo, Neha, Singh, Pooja, Shah, Pratik, Ahmed, Sheaza
• Format: Journal Article
• Language: English
• Published: Quebec International Association of Scientists in the Interdisciplinary Areas 01.12.2014; Springer Nature B.V
• Subjects: Algorithms; Annotations; Biomedical and Life Sciences; Computation; Computational Biology/Bioinformatics; Computational Science and Engineering; Computer Appl. in Life Sciences; Databases, Protein; Format; Health Sciences; Human; Internet; Ions; Life Sciences; Mathematical and Computational Physics; Medicine; Models, Molecular; Molecular Sequence Annotation; Nucleic acids; Original Article; Programming Languages; Protein Structure, Secondary; Proteins; Proteins - chemistry; Software; Statistics for Life Sciences; Theoretical; Theoretical and Computational Chemistry; Three dimensional; User-Computer Interface; Visualization; PDB parser tools; protein 3D structure visualization tools; PDB explorer; PDB
• ISSN: 1913-2751; 1867-1462; 1867-1462
• DOI: 10.1007/s12539-012-0044-x

The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it’s not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in.