- Article -
| In Silico Biology 7, 0022 (2007); ©2007, Bioinformation Systems e.V. |
Analysis of secondary structure predictions of Dengue virus type 2 NS2B/NS3 against crystal structure to evaluate the predictive power of the in silico methods
Rozana Othman1,5*, Habibah Abdul Wahab2,3, Rohana Yusof4 and Noorsaadah Abd Rahman5
1 Department of Pharmacy, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
2 School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
3 Laboratory of Biocrystallography and Bioinformatics Structure, Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
4 Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
5 Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
* Corresponding author
Email: rozanaothman@um.edu.my
Edited by E. Wingender; received September 18, 2006; revised February 08 and March 02, 2007; accepted March 03, 2007; published March 27, 2007
Abstract
Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. Thus, it is plausible that this approach is applicable to the initial stage of structural studies of proteins with low amino acid sequence homology against other available proteins in the PDB.
Keywords: Dengue virus type 2, serine protease, secondary structure prediction, consensus, protein structure