3d molecular modeling:
my graduate coursework in 'advanced molecular modeling' was really helpful to understand concepts in 3d molecular modeling. my research in molecular modeling (guide: professor philip borer, dept of chemistry, syracuse university, ny) comprised proposing a 3d model of unknown protein homologous to glucose 6 phospho transporter (g6pt) protein. i selected a eucaryotic protein based upon maximum sequence homology (~30%) by blasting g6pt protein sequence. template pdb file was downloaded from rcsb and loaded in insightII software. sequence was extracted from pdb file and then a multiple sequence alignment was done across different sequences of the same family from blast including template sequence. alignment was modified based upon chain breaks in template sequences and handed over to modeler software. after first run, energy data from modeler was analysed and alignment of residues with higher energy violations were altered. further energy analysis was done using prosa. modified sequences were handed over to modeler for loop modeling and this procedure was repeated a number of times till a model with minimum energy deviation was obtained. further energy analysis was done to confirm that all the residues fit into highly allowed regions of ramachandran plot. follow the 'read more' link to see comparison between original 3d model of template and 3d model of target i proposed.

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