Abdul Nasir

8 Questions 24 Answers 0 Followers

Questions related from Abdul Nasir

WHy the docked substrate move out from the active site of the protein during MD simulation?

I have docked the substrate in the active site of the protein ( contains NAD and lactate substrate ), interacting with binding residues through hydrogen bonding. When i start the MD simulation...

01 January 2019 6,978 11 View

How to correct the number of coordinates in gromacs file (solv.gro, topol.top)

Respected All, I am going to do the Ligand MD simulation using Justin Lemkul tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/03_solvate.html). After...

01 January 2017 206 4 View

Which statistical test is appropriate for unequal sample size with less mean difference?

I have worked on vocal behavior of rats during a diseased condition and found 8 different type of calls but of unequal size with less difference among means in their temporal parameters despite...

06 June 2016 8,810 3 View

How to calculate Surface electrostatic potential using pymol?

Hi all, please can any guide me on easy way to calculate Surface electrostatic potential of a protein using pymol? or there is any free online server?

01 January 2016 3,069 2 View

What is the relatioship between the potentail energy and protein structure?

I have modeled a wild protein structure and their five mutant structure. Now i have analyzed their potential energy for normal and mutants. Potential energy calculated for wild, Pro420Arg,...

01 January 2016 8,994 10 View

Can anyone explain why I have a failure while running an MD simulation using MOE software?

I am trying to start the MD simulation of the protein (energy minimized at 0.05) using MOE Docking software. But when I run the Dynamics, the software gives a failure that the time step is too...

10 October 2014 9,717 2 View

How to merge two subunit of protein through linker by homolgy modeling?

Hello, I have two subunits (let say alpha and beta) between them a linker sequence (29 amino acid). I have modeled the alpha and beta subunit using templates extracted from PDB. There is no...

01 January 1970 2,917 12 View

How to find the sequences responsible for the aerobic nature of the enzyme through phylogenitic analysis?

Hello, I have amino acid sequences of the same enzyme in more than 150 different organism which is grouped in two form i.e Aerobic and anaerobic enzyme. I did blasting of these sequences but i...

01 January 1970 306 1 View