Olivia Debnath

4 Questions 2 Answers 0 Followers

Questions related from Olivia Debnath

Hey! Is anyone using RINALYZER for computing residue interaction network & interaction scores starting from the protein PDB ID?

RINALYZER uses the RINERATOR module that can predict non-covalent interactions between residues and can represent a protein as a two dimensional interaction graph. I have two queries: a). How's...

07 July 2018 8,436 0 View

What is the most reliable way of doing in-silico mutagenesis (say, mutating or deleting certain amino acids) apart from SCWRL Algorithm?

Suppose, I have the original PDB structure and I need to do certain mutations (may be, substituting amino acids) before performing MD Simulations or Normal Mode Analysis. Are there any reliable...

11 November 2017 776 7 View

While using NotI and NdeI as restriction enzymes, is it necessary to increase the digestion time?

I am using NotI and NdeI to digest a 750 bp insert in a 5400 bp vector backbone. I am hardly getting any colonies after transformation. Once I got plenty of satellite colonies in 3:1 ligation...

10 October 2017 5,028 2 View

How can we increase the ligation efficiency while using NdeI and NotI as restriction enzymes?

The ligation at 4 degree overnight which is an appropriate one for joining short/sticky ends is not working. Should I go for benchtop ligation for 2 hours at RT? Or, do you think the 16 degree...

09 September 2017 9,391 3 View