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

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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...

10 November 2014 6,542 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.

09 October 2014 7,109 6 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...

08 September 2014 4,909 5 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) ?

08 September 2014 5,904 2 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

08 September 2014 5,350 5 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.

05 June 2014 6,829 8 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...

05 June 2014 8,027 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?

05 June 2014 10,032 9 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...

03 April 2014 767 28 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...

03 April 2014 8,851 3 View

Can I use a HisTRAP column for affinity chromatography?

I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...

07 August 2024 505 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

What is the best blank for nanodrop if I want to read a recombinant protein concentration?

Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC

01 August 2024 967 3 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

Venkat Reddy Chirasani

Hi,

you can use "g_vesicle_radius", a customized gromacs tool from http://md.chem.rug.nl/~mara/softa/ site.

Tushar Kanti Ray

You can do so by electron microscopy following negative staining if they are large membrane vesicles. If they are microvesicles, you will have to measure in thin sections at high magnification. There are standard methods in the literature.