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Pipeline publication

[…] m toward pathogens.,– All of the experiment methods were done by using a personal computer with 2.1 GHz Intel Pentium Dual Core, RAM 1 GB, and Windows XP Professional Edition. The experiment was also conducted with the Internet support and several kinds of online and offline softwares., The sequences of hemagglutinin and neuraminidase of H5N1 Indonesian strain were retrieved from Influenza Virus Resource of National Center Biotechnology Information website (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html/)., Following Velkov et al, the mapping of our epitopes has taken into account their tendency of antigenic drifting. The prediction of proteosomal cleavage H5N1 virus was analyzed by using PAPROC-I tools (http://www.paproc.de/), while the transport antigen presentation (TAP) binding was predicted by using TAPPRED server (http://www.imtech.res.in/raghava/tappred/)., Propred and netMHCpan servers were used to identify the bond region on the class I HLA of the antigen.,, The selected epitopes were further analyzed their conformation and stability by performing epitope visualization and molecular dynamics simulation, respectively. All of these steps were completed by using MOE 2008.10 software. The epitope visualization itself was used to determine class I and class II HLA of the selected epitopes. The evaluation of the residues was conducted by counting the free energy minimization for the interactions between HLA and epitope. The 10 ns molecular dynamics simulation was executed in order to observe the interaction and stability between epitope and HLA., Following Vel […]

Pipeline specifications

Software tools PAProC, TAPPred, ProPred, NetMHCpan
Organisms Homo sapiens, Influenza A virus
Diseases Sexually Transmitted Diseases, Viral, Retroviridae Infections, HIV Infections