Suchetana Gupta

4 Questions 5 Answers 0 Followers

Questions related from Suchetana Gupta

What is the best starting structure for a molecular dynamics simulation: a docked structure or a superposed structure?

I am planning to calculate binding affinities for a set of ligands to my protein of interest, both the wild type as well as mutated form. The crystal structure for the particular conformation of...

09 September 2015 9,834 6 View

How do I tackle positive binding energy in simulation?

I have docked a known inhibitor to my protein and the initial docking energy was ~ 5Kcal/mol. I ran 40ns simulation using AMBER and when I performed MMGBSA analysis on this complex, the binding...

08 August 2015 8,969 7 View

How can I get a starting structure to dock a ligand in a homology modeled structure?

I have been successful in generating the homology model of the catalytic region of a chitin deacetylase protein but am facing some difficulties while simulating the protein. (My protein has...

06 June 2015 9,166 6 View

Is there a method to calculate PMF (SMD/Umbrella Sampling) using two reaction coordinates simultaneously (spanning all possible angles and distances)?

Anything in AMBER?

01 January 1970 3,573 1 View