Revathi Sanker

11 Questions 29 Answers 0 Followers

Questions related from Revathi Sanker

Can normal mode analysis differentiate ligand bound and unbound states?

Can anyone suggest normal mode analysis tools that can be used to differentiate 2 states of the protein- in the presence and absence of a ligand?

07 November 2014 4,794 5 View

Is it possible to find out the occupancy of water within a protein using gromacs?

I would like to plot no. of water molecules within a cut-off distance as a function of time. Any gromacs utility that will help me? Thanks in adv

04 September 2014 738 5 View

Is there any tool to measure the radius of curvature for a lipid membrane or protein?

Any gromacs utility to measure radius of curvature? How is it different from the radius of gyration?

07 August 2014 7,286 2 View

Is anyone aware of names of proteins that show large bending movements that are functionally relevant?

I would like to get the names of a few proteins that show bending dynamics in solution. Are there any transport proteins that shown similar movements? Kindly post them here. Thanks in advance.

13 June 2014 6,770 7 View

What is the energy barrier from hinge movements (like bending and twisting) in proteins?

In two domain proteins there are movements possible along the hinge. Is anyone aware of the energy involved in this hinge movement?

13 June 2014 4,257 8 View

Is anyone familiar with the methodology/tool to calculate twisting in proteins?

I wish to calculate the extent of twisting that my protein undergoes. Is there a tool/script/software that will enable this calculation? It is a beta barrel domain of the protein that is...

07 April 2014 5,867 3 View

What is the relationship between MMPBSA (or docking binding energy) and experimental IC50?

I have computed the binding energy of my protein to the ligand, initially by docking and after MD by MMPBSA. How do I relate these binding energy values to experimental IC50 that is reported in...

05 April 2014 7,239 12 View

How do you compute rmsd using ptraj in Amber software?

How do I specify this in the mask for AMBER ptraj? Protein residues are from 1-400. But I want to leave out two loop regions,100-105 and 250-255. The RMSD plot fluctuates and I presume leaving out...

01 April 2014 7,049 27 View

How do we choose the optimum value of the spring constant k and pulling velocity in steered MD simulations?

I wish to perform steered molecular dynamics for an inhibitor pull-out study. Some papers choose a range of spring constant(k) and velocity(v) and finally choose one combination while other papers...

18 March 2014 7,443 17 View

For performing linear interaction energy analysis, is it necessary to simulate the free ligand for the same time as that of the complex?

In NAMD- linear interaction energy, we perform two sets of simulations- protein+ligand complex in water and free ligand in water. If I have performed my simulation of the complex for 100ns, is it...

13 January 2014 5,449 2 View

I wish to compute binding energy in a protein-ligand system. My simulations were done using NAMD-CHARMM36. Could anyone suggest tools for analysis?

Conventional MMPBSA is not suitable as the forcefield will vary in amber. I do not have access to CHARMM software in our lab. Is there any other way I could compute the strength of interaction...

10 January 2014 8,266 2 View