3D structural modeling of HIV-1 GAG protein

• Main Author: Xu, Xiao Yan.
• Other Authors: Kwoh Chee Keong
• Format: Final Year Project
• Language: English
• Published: 2011
• Subjects: DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
• Online Access: http://hdl.handle.net/10356/46424
• Institution: Nanyang Technological University

This report is written to provide a detail description of the Final Year Project- Three Dimensional Structural Modeling of HIV-1 GAG Protein. This report will highlight the author’s effort in the Final Year Project: 3D Structural Modeling of HIV-1 GAG. There are a three main section in this project. Firstly, to model the 3D Structural view of the original GAG sequence and 9 others mutated GAG sequence. All the sequences are modeled using two different modeling software, I-TASSER and MODELLER. Secondly, the best models from both the modeling software will be selected to compare in two ways. First way is to compare within the software itself, to observe the 3D structural view difference of the 9 mutated sequences. The purpose of this comparison is to analyze how different is the mutated sequence to the original sequence. Second way, two existing tools, namely I-TASSER and MODELLER will be studied and results will be consolidated and will be used to analyze, compare and distinguish which of the tool will contribute a more accurate protein structure prediction. Energy Calculation from SwissPdbViewer is used to compare between the tools. Lastly, all the results of the models including all the comparison will be display in a web interface. I-TASSER is concluded as a better modeling tools as compare to MODELLER. This may due to the huge GAG sequence with 500 residues. I-TASSER may have a bigger database to identify the templates for it’s modeling; on the other hand MODELLER is run manually and thus may have some limitation in the number of templates available for its modeling. Thus I-TASSER is a better modeling tool for large sequences. As for the Structural Mutation of GAG, further research in this area is required to have biological evidence to support that outcome.