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Mammalian Biology: Structural and Computational Biology
Location :International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
Activities:The Structural Biology Group consists of two independent faculties with combined expertise in bioinformatics, protein biochemistry and protein crystallography. The group aims at understanding the structural principles that govern protein-based bio-molecular interactions. Structure-function studies on several important malaria parasite proteins are currently under way. Our laboratory uses multi-disciplinary techniques within modern biology, including biochemistry, bioinformatics, cell biology, parasitology and protein crystallography, to unravel the mechanism of action of important parasite proteins. Over the past few years, we have made progress in understanding various parasite proteins involved in erythrocyte invasion, hepatocyte invasion and gametocytogenesis. We have solved crystal structures of novel proteins from each of the above stages of the parasite life cycle. Structure-based functional analysis of proteins involved in above processes is being pursued. We have also established a “state-of-the-art” protein crystallography unit at ICGEB New Delhi where diffraction data can be collected and processed for structural analysis. Recently, we initiated in silico inhibitor discovery program for the parasite proteins of interest. The objective is to utilise crystal structure information for discovery of novel inhibitors using structure-based computational approaches. For this purpose, advanced molecular visualisation, modelling and computational software has been installed in the laboratory. The long-term goal is to evaluate the performance of computational techniques in discovering novel inhibitors. The bioinformatics laboratory is equipped with high performance computers consisting of servers, workstations and clusters for parallel computing. In the bioinformatics laboratory, we have created a database of protein models for Plasmodium falciparum, which has been incorporated into the PlasmoDB database. Comparative analysis of structures of host and parasite proteins has yielded information about proteins that are different from parasite proteins. We are currently characterising, on an experimental level, one such parasite specific protein, a proteasome protein named HslV in the parasite. We have also created a database ProtRepeatsDB, a database of different types of protein repeats in genomes for which complete protein sequences are available. The relational database aids in comparative analysis of different types of amino acid repeats in genomes. We are also interested in studying cell cycle regulating proteins- cyclins, using Artificial Intelligence (AI) techniques. We have already developed a SVM (Support Vector Machine) based method for prediction of cyclins in different genomes. Other research interests of the bioinformatics laboratory include comparative genomics to identify regulatory elements like miRNAs and transcription factors in genomes.
Keywords:Bioinformatics, molecular modelling, protein crystallography