Determination of tDETERMINATION OF 3D STRUCTURE OF GAG POLY PROTEIN ISOLATE 90CF056 OF HIV TYPE 1 BY HIDDEN MARKOV MODEL AND NEURAL NETWhree dimensional structure of Gag Poly Protein isolate 90CF056 of HIV type 1 by Hidden Markov Model and neural networks

Introduction: The study of understanding the structural and molecular conservation of HIV-1 Gag function has revealed a number of potential Gag-related targets for possible therapeutic intervention. In this study, we emphasize that our current understanding of HIV-1 Gag poly protein suggest some approaches to be as a target for novel drugs. Objective: The functional conservation of HIV-1 Gag indicates rational drug design taking Gag as he drug target1.HIV-1 may be blocked by targeting gag poly protein. This could proffer new scheme for novel drug classes that could complement current HIV-1 treatment options. Methods: The crystal structure of Gag poly-protein is unavailable. The templates similar are much smaller in size and thus ab-initio method is applied to determine the three dimentional structure of gag poly-protein. The value given in the program is an approximation of the probability as provided by the software with neural networks. The predictions are designed to be limited, to a score >=.18 which is actually an approximation of the probability. The predictor is an artificial neural network. NN: Inputs indicates inclusion of separation and sequence length, e-value statistic which are based on mutual information values, a statistic based on propensity of residues in contact with each other. Results: The local structure predictions are performed with neural networks for several different local structure alphabets, and hidden Markov models are created. Conclusion: The complete three-dimensional model of the Gag poly protein is constructed by fold recognition and alignment to proteins in the Protein Data Bank is done