Journal of
Computational Biology and Bioinformatics Research

  • Abbreviation: J. Comput. Biol. Bioinform. Res
  • Language: English
  • ISSN: 2141-2227
  • DOI: 10.5897/JCBBR
  • Start Year: 2009
  • Published Articles: 39

Full Length Research Paper

In silico structure assessment analysis of core domain of six protein data bank entries of HIV-1 Integrase

Salam Pradeep Singh* and B. K. Konwar
Bioinformatics Infrastructure Facility, Department of Molecular Biology and Biotechnology, School of Science and Technology Tezpur University, Tezpur 784028, Assam, India.
Email: [email protected]

  •  Accepted: 25 October 2011
  •  Published: 31 January 2012


HIV integrase is a 32 kDa protein produced from the C-terminal portion of the Pol gene product, and is an attractive target for new anti-HIV drugs. Its main function is to insert the viral DNA into the host chromosomal DNA, a step that is essential for its replication. However there are six different Protein Data Bank (PDB) entries of the same protein with the same amino acids with PDB IDs 1BIS, 1BIU, 1BIZ, 1HYV, 1HYZ and 1QS4. The present work focuses on the structure analysis of chain A of the different PDB entries of the same protein using in silico approaches via the Swiss Model structure assessment server, ANOLEA Assessment server and Ramachandran plot analysis. The structure assessment analysis reveals that there is a major difference among these PDB entries based on the energy assessment and structural analysis. The PDB ID 1BIU chain A is found to be the most stable and reliable structure for assisting computer aided drug designing.


Key words: In silico structure, core domain, protein data bank, HIV integrase.