Suchetana Gupta

4 Questions 9 Answers 0 Followers

Questions related from Suchetana Gupta

While checking stability of a modelled protein (unliganded), what range of RMSD is acceptable?

We have a modelled protein structure (unliganded), about 470 amino acids in length. On running ~70ns production run, we notice the RMSD plot reaching a plateau at ~5A. Is this an acceptable value?...

02 January 2017 9,092 4 View

How do I perform MMGBSA analysis for a metalloprotein containing Co using Amber?

I have 60 ns simulation of a metalloprotein bound to its substrate. I wish to perform MMGBSA analysis to find out the interacting residues. When I tried the usual method using mmgbsa suite in...

10 August 2015 8,356 5 View

How do I compare the interactions between a protein and two inhibitors from my 30ns all atomic trajectory?

Ideally I would like to compare the interactions that the two inhibitors make with the protein over the entire trajectory (I ran my simulation in AMBER). I know cpptraj has the option for doing...

20 May 2015 8,258 8 View

How do I decide if I need to apply a restraint to the inhibitor in a protein-inhibitor complex simulation?

I want to study the interactions of an inhibitor (which is a substrate mimic) to a protein. It is a reversible inhibitor, thus, does not form any covalent bond to the protein. I started with a...

04 April 2015 569 5 View