Revathi Sanker

18 Questions 41 Answers 0 Followers

Questions related from Revathi Sanker

Could anyone suggest suitable tools to plot protein contact maps?

My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of...

11 November 2014 6,506 9 View

Radius of gyration as a measure of protein compactness - does it apply to only globular proteins?

Can the changes in radius of gyration of elongated protein also tell the compactness of the protein? If yes, is a difference in Rg of 30 A significant? Thanks in advance.

10 October 2014 7,074 6 View

Do all proteins with a beta- barrel (Fec A transporter) or half beta barrel (cystatin) necessarily twist?

What could be the molecular basis for the protein to twist and undergo a conformational change intrinsically (that does not involve any substrate binding event) ?

09 September 2014 5,873 2 View

Can anyone assist me with adding probability of state on the projection of eigen vector PC1 vs PC2 plot in gromacs?

I have performed the principal component analysis in gromacs and I have obtained the projection of eigen vectors PC1 vs PC2 plot as in figure 4BI would like to add information about the...

09 September 2014 4,870 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

09 September 2014 5,323 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?

08 August 2014 3,789 2 View

How can I deal with the substrate moving out of the box during MD simulation?

I have simulated an elongated protein in a cubic box (reason being the long edges of the protein tilt during simulation and interact with its periodic image thus resulting in bad energy values...

06 June 2014 7,977 5 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?

06 June 2014 9,990 9 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.

06 June 2014 6,784 8 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...

04 April 2014 711 28 View

Is g_sham the utility to use to compare the free energy profile of the inhibitor vs substrate bound protein?

In order to compare the free energy landscape for a protein under two conformations- substrate vs inhibitor bound, will g_sham give me the required FE landscape?

04 April 2014 1,642 2 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...

04 April 2014 8,805 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...

04 April 2014 7,208 12 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...

03 March 2014 8,108 17 View

What is the difference between steered molecular dynamics, umbrella sampling, and adaptive biasing force technique?

Can anyone explain the difference between these three advanced molecular dynamic techniques?

03 March 2014 5,578 0 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...

01 January 2014 4,179 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...

01 January 2014 3,709 2 View

In an MD simulation study, to capture the protein dynamics, I am seeing the conformational change in less than 30ns. Should I extend the simulations?

These days simulations are performed for over 100ns easily. Will a 30ns data still be valid?

12 December 2013 8,502 15 View