In silico analysis

Jenkins, J. A., Griffiths-Jones S, Shewry, P.R., Breteneder, H. and Mills, E.N.C., Structural relatedness of plant food allergens with specific reference to cross-reactive allergens An in silico analysis. J. Allergy Clin. Immunol., 115, 163, 2005. 

In C. Clementina Hort. ex Tanaka x C reticulata, Blanco (fortune mandarin), two PAL genes (AJ238753 and AJ238754) were isolated from a flavedo cDNA library and subsequent Southern blot analysis confirmed that two or more copies of the gene were present in the genome [28]. In silico analysis of expressed sequence tags (ESTs) from C. sinensis (L) Osbeck identified three putative PAL isoforms in this species [29]. Most species analyzed to date (reviewed in 30, 31) have also shown that PAL is encoded by a multigene family. 

Citrus species are well-known for their accumulation of flavone- and flavanone-glycosides, and thus should contain all of the enzyme activities necessary for the synthesis of these compounds. Two tentative consensus sequences for FNS-II have been identified by in silico analysis of the CitEST database, apparently representing the first identification of putative FNS-II genes in this genus [29]. Biochemical determination of function and analysis of the proteins encoded by these genes will be an important step toward elucidating flavone synthesis in Citrus. 

A comprehensive in vitro and in silico analysis of antibiotics that activate PXR and Induce CYP3A4 in liver and intestine. Drug Metabolism and Disposition the Biological Fate of Chemicals. 

Gleeson, M.P. (2007) Plasma protein binding affinity and its relationship to molecular structure an in-silico analysis. Journal of Medicinal Chemistry, 50, 101-112. 

Le Bihan, T., Robinson, M. D., Stewart, 1. L, and Figeys, D., Definition and characterization of a trypsinosome from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures. Journal of Proteome Research 3(6), 1138-1148, 2004. 

Yousef GM, Borgono CA, Popalis C, et al. In-silico analysis of kallikrein gene expression in pancreatic and colon cancers. Anticancer Res 2004 24 43-51. 

Ghosh, D. and Gupta-Bhattacharya, S. 2008. Structural insight into protein Tl, the non-allergenic member of the Bet vl allergen family—An in silico analysis. Mol Immunol 45(2) 456 162. 

Recently, Pridmore and co-workers (2008) have examined the production of hydrogen peroxide by the human gastrointestinal isolate Lactobacillus johnsonii NCC533. Through in silico analysis of the genome of this potential probiotic strain they identified the means by which hydrogen peroxide is synthesized. Furthermore, they demonstrated that the strain actively produced hydrogen peroxide in vitro at levels that were inhibitory for S. Typhimurium. 

Mulder, N., Phan, I., Servant, F., Apweiler, R. (2003). The Proteome Analysis Database a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31, 414417. 

Mazhari R, Greenstein JL, Winslow RL, Marban E, Nuss E1B. 2001. Molecular interactions between two long-QT syndrome gene products, 1TERG and KCNE2, rationalized by in vitro and in silico analysis. Circ. Res. 89 33-38... 

---