Naiju Thomas

8 Questions 9 Answers 0 Followers

Questions related from Naiju Thomas

During transduction, when blasticidin was added to media containing doxycylcine, I saw 90% cell death. Why?

In 60mm dish containing Cas9 LapC4 cells, I added 3 uL each of doxycycline (1 mg/mL) and blasticine (10 mg/mL), suddenly the cells went into shock and started floating. This has not been the case...

29 August 2019 7,942 3 View

Can we add amino acids to the 3d protein crystal structure from PDB?

A dimer protein crystal structure of my interest is not having 72 amino acid, but its monomer is having the full amino acid sequence. Is it possible that I can add those missing amino acid in the...

23 May 2018 2,160 5 View

If a ligand binds at a hinge between two protein domains, what are the chances that this interaction will deny the movement of protein based on hinge?

While docking my ligand was found to bind on a hinge between 2 protein domain, which is 9 AA long and helps in the movement of one domain. Can it be hypothesized that due to the formation of...

12 March 2018 8,610 0 View

What is the probability of a ligand binding with particular protein in multiple viruses?

I was trying to dock a ligand to 2 viral protein at first and got good binding properties at very important binding sites of virus, but when I tried to dock with other 15 viruses, saw type of...

09 February 2018 2,306 2 View

What is the significance of X in a sequence while doing multiple alignment?

While doing multiple alignment in MEGA7, I found that particular country had lots of X coming in the viral genome sequence, which lead to a difficulty in getting an output by aligning them. How...

06 February 2018 934 1 View

Does the ligand conformation with lower energy useful if, it bind at very important site?

a plant compound was used against virus to stop the attachment of virus on the cell (in-vitro) and experimentally proved also that but the exact mechanism was not found for this. I did a blind...

23 January 2018 3,443 2 View

How to get a log.txt file after docking in AutoDock Vina?

I did docking in AutoDock Vina and result had only best docking energy and RMSD, but no log file is generated. I want VDW energy, Interaction energy and electrostatic interaction energy. How to...

04 October 2017 2,428 3 View

How to visualise the output from Autodock Vina in ligplot to find the AA interactions?

The result of Autodock Vina is an output.pdbqt file, which is having only the ligand pose but no protein structure to which this ligand has docked to. If this file is opened in PyMOL and protein...

13 September 2017 3,857 8 View