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Protein Structural Modeling of Acetylglutamate Kinase from Leptospira Interrogans and Docking Studies of N-Acetyl-L-Glutamate

出版	SSRN, 2009
URL	http://books.google.com.hk/books?id=fXrizwEACAAJ&hl=&source=gbs_api

註釋Acetylglutamate kinase (EC 2.7.2.8) is an enzyme that catalyzes the chemical reaction ATP N-acetyl-L-glutamate ADP N-acetyl-L-glutamyl 5-phosphate. We created a model of acetylglutamate kinase enzyme 3D-structure as template with Molsoft ICM v3.5 software. The Internal Coordinate Mechanics (ICM) homology modeling algorithm has demonstrated excellent accuracy in blind predictions. Moreover, recent results showed that models built with as little as 35% identity can be accurate enough to be successfully used in receptor-based rational drug design. The closest homologue with the highest sequence identity of 38% was selected as a representative model using Yet Another Scientific Artificial Reality Application (YASARA) tools. The model was validated using protein structure checking tools such as PROCHECK (Protein check) for reliability. A total of two pockets were predicted by the software. Once the pockets were predicted, the ligand was subjected to docking reaction using the docking module of Molsoft ICM-Pro software. Based on the Root Mean Square Deviation (RMSD) and energy values, the best docking orientation was selected. The better RMSD value of docking was 0.571201. This study will be used in broad screening of inhibitors of the protein and can be further implemented in future drug designing.