HIVcoPRED: is a web server developed for predicting the coreceptor usage by HIV-1. It takes amino acid sequences of Variable loop (V3) of gp120 protein of HIV and predicts the coreceptor used by the HIV strain. The input query sequences should be submit in fasta format. This prediction server is based on two models : Split Amino Acid Composition (SAAC) and Hybrid approach (SAAC+BLAST)- which integtares the two methods (SAAC and Blast) to predict the final results i.e coreceptor usage.
Human Immunodefiency Virus type1 (HIV-1) infects Human immune system mainly T-helper and Macrophases. The surface protein (gp120) of HIV interacts with CD4 present on human cells and form the primary interaction. The gp120 undergoes with conformational change and the variable loop (V3) exposes to interact with chemokine receptors (CCR5 or CXCR4). The HIV strains which uses CCR5 as coreceptor are known as "R5-tropic", which uses CXCR4 are called "X4-tropic" and the strains which can use both of the coreceptors are called "R5X4-tropic".
The Variable loop 3 is a 35 (mostly) amino acids long peptide with Cysteine on both the ends. The various features of V3 e.g. sequence, net charge etc play very significant role in determining coreceptor usage by HIV. After V3 loop interaction with either of the coreceptors, gp41 protein of HIV undergoes conformational changes and mediates cell membrane fusion of HIV and human cell.
Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India