| Assay Method Information | |
| | Molecular Docking |
| Description: | The docking and scoring of ligands with CAMKIV protein was accomplished using ParDOCK module of Sanjeevini drug design suite, which is based on physicochemical descriptors.[Jain et al., FEBS Lett., 579:6659] We used the atomic co-ordinates of CAMKIV modeled previously.[Hoda et al., J. Biomol. Struct. Dyn., 34:572] Ligand molecules designed by chemical modifications of pyrimidine scaffold are listed in Table S1. We used a rigid docking module computed in several computational steps including preparation of reference protein complex and ligand in a force-field compatible manner as an input file. Docking of ligand molecule at the active site cavity of CAMKIV was performed by using all-atom energy-based Monte Carlo algorithm, which minimizes and scoresthe docked complex. The docked complexes were further minimized using the parallel version of sander module of AMBER;[Pearlman et al., Comput. Phys. Commun., 91:1] predicted binding free energy of docked poses is obtained using Bappl/BapplZ scoring function.[Gupta et al., Protein PEpt. Lett., 14:632] The crystal structure of complex CAMKIV protein in complex with 4-amino(sulfamoyl-phenylamino)-triazole-carbothioic acid(2,6-difluoro-phenyl)-amide(PDB ID 2W4O) was utilized as reference. |
| Affinity data for this assay | |
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