Shakeel Jameeluddin Abbassi

6 Questions 1 Answers 0 Followers

Questions related from Shakeel Jameeluddin Abbassi

During analysis of in silico thermal denaturation of a dimeric protein should I calculate RMSD, RMSF, etc of individual monomers or the whole dimer?

Protein is a homodimer. Which approach would be more appropriate?

05 July 2016 676 1 View

Does a weak affinity for ATP by an enzyme confirm anabolic role?

Based on affinity towards ATP can we determine anabolic or catabolic role of an enzyme?

13 May 2015 1,640 2 View

How do I present relevance of numerical values like kcat, Km etc. in a biological system?

How can we present the relevance of numerical values like kcat, Km etc of an enzyme in a biological system?

18 March 2015 8,367 2 View

How can we place water molecules within the catalytic site during docking?

I want to dock my enzyme with ATP along with water molecule within the distance of around 5 Angstrom.

05 March 2015 9,518 2 View

How can I calculate binding free energy between protein and ligand during protein+ligand complex (GROMACS) md simulations?

I have done an MD run of a protein with ATP using CHARMM force field. I want to calculate binding free energy, which commands can I use for the above. Any suggestions. Thank you.

04 March 2015 3,305 6 View

In protein ligand simulation using gromacs, how to extract both protein and ligand together to visualize the complex in VMD?

I have simulated protein ligand complex but I am unable to extract both the protein and ligand together.

04 June 2014 7,668 2 View