The Bioinformatics materials and goodies
Here in this section, I provide the abstract of my scientific articles, which has been published in peer reviewed scientifc journals. If you want the full version, just access the provided link. Tx.

  1.Title: In Silico Analysis of Envelope Dengue Virus-2 and Envelope Dengue Virus-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method
     Author: Usman Sumo Friend Tambunan, Arli Aditya Parikesit, Hendra, Rizky Ichsan Taufik, Fitri Amelia and Syamsudin
    Source: OnLine Journal of Biological Sciences 9(1): 6-16 , 2009
Problem statement: Dengue fever, which was caused by Dengue virus infection, had became a major public health problem in the tropic and subtropical countries. Dengue virus (DENV) had four serotypes (DENV-1, DENV-2, DENV-3 and DENV-4), based on their immunogenic in the human body. Preventive measure will be necessary to decrease the prevalence of dengue fever, by developing modern vaccine. Approach: This research was focused on in silico study of dengue virus vaccines, by using envelope (E) protein of DENV-2 and DENV-3 as their backbones. T cell epitope prediction was determined by using MULTIPRED server and B cell epitope prediction was determined by using Conformational Epitope Prediction server (CEP). Homology modeling study of E DENV-3 protein as the vaccine backbone had produced six dengue vaccine peptides (HMM Vaccine 1-6). Moreover, homology modeling study of E DENV-2 protein as vaccine backbone had produced six dengue vaccine peptides (ANN vaccine 1-6). Results: The BLAST analysis of HMM and ANN vaccines had produced 93% and 91% identity, respectively. The Ramachandran Plot of both vaccines had shown less than 15% non glycine residue in the disallowed region, therefore it showed the solid stability of the proteins. The VAST analysis of E DENV-3 backbone vaccines had determined, that HMM4 and HMM6 had the highest structure similarity with native E DENV-3. HMM4 and HMM6 had the highest VAST score of 64.5. Moreover, the VAST analysis of E DENV-2 backbone vaccines had determined, that ANN1, ANN3, ANN4, ANN5 and ANN6 had the highest structure similarity with native E DENV-2. ANN1, ANN3, ANN4, ANN5 and ANN6 have the highest VAST score of 64.7. Conclusion/Recommendation: It could be inferred from this research that HMM4; HMM6; ANN1; ANN3; ANN4; ANN5; and ANN6 were the best in silico vaccine design, based on their similarity with native E DENV Proteins. This research could be applied for the wet laboratory and computerised vaccine design.

Complete article, click here 

2. Computational Study of Post Translation Modification in Chimeric Virus Like Particles Vaccine of Human Papilloma Virus with Virion Capsid L1

Usman Sumo Friend Tambunan1, Arli Aditya Parikesit1, Theo A. Tochary1, & Dedy Sugiono1

1. Department of Chemistry, Faculty of Science, University of Indonesia, Depok 16424, Indonesia
The Human Papillomavirus (HPV) infection has a tight correlation with the incidence of cervical cancer. Chimeric virus like particles (cVLP) has been developed as vaccine candidate for preventing cervical cancer. cVLPs are improvement of Virus Like Particles (VLP) by substituting the epitope of L1 HPV -18 and -52 protein to L1 HPV -16 protein. They are ANN1, ANN2, HMM1, and HMM2. The impact of post translation modification will be determined. Based on In Silico study, the dominant post translation modification is glycosylation.

keywords: cVLP, HPV, Cervical Cancer, Vaccine, Post Translation Modification, host

Complete full article click here

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