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Questions related from Atul Pawar
I want to know, whether a particular PDB structure has any calcium binding pockets or residues. It is already bound to a calcium ion in PDB, so I want to simulate it at a particular conc. of...
17 April 2013 1,014 9 View
I have done homology modelling and then refined the model with MD in gromacs. Then I did clustering of trajectories and selected the average structure of the model. Finally I did energy...
25 January 2013 7,241 12 View
I have MD simulated a homology model in gromacs. I have obtained an RMS fluctuation graph for the same. Can this graph be compared with a PDB file which has b-factors generated during X-ray...
25 January 2013 1,791 1 View
i have a papain-like protease but having Chymotrypsin-like activity due to non-canonical active site Serine. I have to find inhibitors for this protease with in-silico methods. Can i dock...
21 January 2013 9,351 3 View
I want to get the psi and phi angles on a particular residue and plot them on ramachandran plot. I went through some tutorials and was informed to use ndx file for that. But can someone give me an...
20 January 2013 2,350 5 View