Computational protocol: Identification of Cellular Calcium Binding Protein Calmodulin as a Regulator of Rotavirus A Infection during Comparative Proteomic Study

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Protocol publication

[…] Putative CaM binding site was predicted in CaM target database (http://calcium.uhnres.utoronto.ca/ctdb/pub_pages/search/index.htm) using the protein sequence of VP6 gene of RV strain SA11 (Accession number AEI91047). Result output is shown with numerical value where series of 9 means highly significant position and the value reduces gradually with decrease in significance . X-Ray crystallographic structure of RV-VP6 monomer was downloaded from (http://www.rcsb.org/pdb/explore.do?structureId=1QHD) and binding sequence analysis was done by Pymol (V 1.01). Trimeric 3-D reconstructive structure of RV-VP6 was taken from (http://pdbj.org/emnavi/emnavi_detail.php?id=1752) and binding site was analyzed by UCSF-Chimera. […]

Pipeline specifications

Software tools PyMOL, UCSF Chimera
Databases CTDB PDBj
Application Small-angle scattering
Organisms Mus musculus, Homo sapiens
Diseases Infection, Rotavirus Infections, Tetralogy of Fallot, HIV Infections
Chemicals Calcium