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Title: Homology modeling and docking studies between HIV-1 protease and carbamic acid
Authors: Balakrishnan, M
Srivastava, R C
Pokhriyal, Mayank
Keywords: Docking, energy minimization
HIV
homology modeling
protease
RMSD
Issue Date: Jan-2010
Publisher: CSIR
Abstract: HIV-I protease (HIV-I PR) is aspartic protease enzyme which is essential for the life-cycle of HIV retrovirus. Homology structural model and function relation of HIV-I PR have solved the structure of HIV-I proteases. We created a homology model of HIV-I PR and the 3-D structure as template using with ICMPro software. The ICMPro homology modeling algorithm has demonstrated excellent accuracy in blind predictions. Moreover, recent results show that ICMPro 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 38.395% was selected as representative model using YASARA tools. The model was validated using protein structure checking tools such as PROCHEK 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 ICMPro software. Based on the RMSD and energy values, the best docking orientation was selected. The better RMSD value of docking is 0.0066288. This study will be used in broad screening of inhibitors of the protein and can be further implemented in future drug designing.
Page(s): 96-100
ISSN: 0975-0967 (Online); 0972-5849 (Print)
Source:IJBT Vol.09(1) [January 2010]

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