Pallabi Sengupta

4 Questions 6 Answers 0 Followers

Questions related from Pallabi Sengupta

How to circumvent the frequent fatal errors stating "atoms do not have a type" while making the prmtop and inpcrd files in AMBER?

I was trying to simulate a docked complex of peptide and DNA. The DNA .pdb file was developed in Schrodinger and the peptide .pdb files are modelled based on the solution NMR structure in CYANA....

08 August 2016 6,017 4 View

Why does Hydrazine cleave at A and G bases instead of C and T in CT ladder sequencing reaction?

We performed DMS footprinting of a 90 nt sequence. The left most lane is A+G ladder. The 2nd and 3rd lane denote DMS reactions in different conditions which are consistent with our hypotheses. The...

01 January 1970 6,583 0 View

How to estimate negative superhelical density in plasmid DNA?

I am working with ~6000 bp plasmid DNA, which contains the promoter of my interest. This promoter has a cis-element, which forms non-canonical DNA structures in cells, which I have already proved....

01 January 1970 3,607 1 View

How can we deconvolute the CD spectra of nucleic acids?

There is a handful of webservers to deconvolute the CD spectra of peptides and proteins. I am particularly looking for deconvoluting DNA CD spectra for detailed analysis of the thermal melting...

01 January 1970 6,492 0 View