This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In this project, an optimal secondary structure of herpes simplex virus type 1 glycoprotein K(gK) and the UL20 protein (UL20p) will be obtained by using computational approaches. Each of the employed algorithms produces specific secondary structural information;however, in most cases, these predictions do not entirely agree with each other. We wish to derive the best combination of currently available algorithms that can arrive at an optimum secondary structure prediction. Ab initio protein modeling, comparative protein modeling and side chain geometry prediction will be used to predict the secondary structure of gK and UL20p. An important aspect of the work is that the secondary structures of UL20p and gK will be predicted for all available gK and UL20p homologs encoded by different alpheherpesviruses. This analysis will allow the delineation of specific structural features that are conserved among all gK and UL20p homologs. We have predicted the secondary structure of UL20p and gK using 12 computational methods. Results from the 12 packages were analyzed and compared. Further work includes predicting the secondary structure of all gK and UL20p homologs and delineating the structural features of these homologs.
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