How can I calculate center of mass for a protein?

Hello every body I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on. pleas give me a full help. thanks

31 December 2017 328 8 View

How can you calculate salt bridges and hydrogen bonds for a specific part of the structure in throughout a trajectory?

Hello every body I want to calculate the pattern of salt bridges and hydrogen bonds between two specific part of the protein througut the for the 10 last ns of a gromacs simulation trajectory....

31 December 2017 217 3 View

How can I calculate antrophy using gromacs?

Hello every body I want to calculate the antrophy amount of a protein-protein complex using gmmpbsa module of gromacs. I can calculate binding energy but not antrophy. If you have any...

11 December 2017 8,649 1 View

How should i define a calcium in pdb file?

hello I have a protein with a calcium ion. I edited the PDB file, renaming the calcium to CA, as atom name and atom type and pdb2gmx, runs successfully. but know I worry becuse some viewers...

01 February 2017 6,703 0 View

Could any one help me in peptide expression?

I want to express a 37 a.a, 43 a.a and 55 a.a peptides using pET His6 Sumo TEV expression vector with BioBrick polypromoter restriction sites (14-S). the vector host is XL1 blue and the company...

08 September 2016 5,212 3 View

How can I calculate the dihedral angle change of two helices using amber scripts?

I need to know the position of two helices in a structure in comparison to each other. so I should to calculate the variation of their dihedral angles versus time. there is an article in the...

05 June 2016 9,713 2 View

How could i get a free clash avarage structure from gromacs trajectory?

hello I have 200 ns simulation of a peptide and i want to calculate average structure of the simulation. I used this command: g_rmsf -f md.xtc -o rmsf.xvg -s md.tpr -ox av.pdb The resulting pdb...

05 June 2016 323 4 View

How can i designe a harker diagram for a tow atom crystal system?

I have a hard exam in x-ray crystallography. i need your help to pass it. i need a reference to understand phase problem solving. any help is appreciated.

04 May 2016 3,241 1 View

How could I refold Denileukin diftitox(ontak) after extraction?

Hi is there any instruction to refold Denileukin diftitox(ontak)? it is really vital for my project. every help is appreciate.

09 October 2015 4,923 0 View

How can I set the pressure in NPT phase of molecular dynamic simulation?

We could set temperature with kinetic energy in MD. How about pressure in NPT phase?

31 December 2014 8,167 8 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

No title

02 March 2021 3,060 3 View

Does Napabucasin soluble in dichloromethane and in ethanol?

I need to prepare a solution of Napabucasin (inhibitor of cancer cell stemness) in dichloromethane. The drug is expensive, so maybe somebody already tried to do it. If it is soluble, what is the...

02 March 2021 9,945 3 View

Issues with Permeabilization during Flow Cytometry?

Hello Everyone. Currently I am working to characterize macrophages in the myocardium after ischemia-reperfusion injury in rats. Due to the low total cell number isolated from rat hearts I can...

01 March 2021 3,867 3 View

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

01 March 2021 8,087 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View