Paper Citing NAMD - Abstract
Arora, Neelima; Banerjee, Amit Kumar; Murty, U. S. N.
In silico Characterization of Shikimate Kinase of Shigella flexneri: A Potential Drug Target
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2:280-290, SEP 2010
Shigella flexneri is a major pathogen responsible for Shigellosis causing massive morbidity among young population and imposes huge socio-economic burden. In this study, Shikimate Kinase (SK) from S. flexneri was characterized in silico and disordered regions were predicted. Motifs and domains were calculated using computational tools. A three dimensional model of Shikimate Kinase of S. flexneri was constructed using Shikimate Kinase of E. coli (PDBID: 1KAG_A) as template by comparative modeling approach. Molecular dynamics calculations were carried out to check the stable conformation embedded in water sphere with least RMSD possible. Perusal of backbone conformation of the modeled structure by PROCHECK revealed that more than 98% of the residues fell in the allowed regions and ERRAT results confirmed good quality of modeled structure. Active site and its important residues were predicted for the derived model. Disulphide bridges were estimated by computational method and most probable pattern of cysteine residues was found in the pairs 8-22. Results of this study will shed light on the structural aspects of Shikimate Kinase of S. flexneri and will aid in rational drug designing.
