Najme Dehghanbanadaki

20 Questions 27 Answers 0 Followers

Questions related from Najme Dehghanbanadaki

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

01 January 2018 473 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....

01 January 2018 299 3 View

Could i treat different stages of cancer cell line with the same drug?

Hi every body I work on Wnt/beta catenin signaling pathway. I have a drug which is effective on non metastatic SW480 cell line. I want to test it on metastatic cell line SW620. the pathway is...

12 December 2017 1,712 4 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...

12 December 2017 8,725 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...

02 February 2017 6,775 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...

09 September 2016 5,288 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...

06 June 2016 9,813 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...

06 June 2016 419 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.

05 May 2016 3,319 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.

10 October 2015 4,999 0 View

What are thermodynamic aspects of living systems?

could you pleas explain thermodynamic laws of living system for me? is there any different between entropy of healthy and disease tissues?

01 January 2015 4,415 1 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?

01 January 2015 8,238 8 View

Which component of canonical wnt signalling are over expressed in pc-3 and hs578t cell lines?

Is wnt3a overexpressed in pc3 cell lines? is there any helpfull article about expression profile of these cells?

09 September 2014 6,677 3 View

Which calcium buffer do you propose to treat cells with?

I have a calcium-dependent protein. I should treat my cells with that but I don't know which buffer is the best. Someone advised me to use a ca-EGTA buffer, but I think it is harmful for my cells....

06 June 2014 9,838 7 View

How to extract force constant from output file of Gaussian for specific bonds?

I optimized my structure and calculated the frequency of that. I used Gauss view but need a command or instruction to calculate the exact force constant for my interested bonds.

06 June 2014 7,473 0 View

Can anyone help me to find the force constant of a special bonds in Gaussian?

I have problems with calculation of the interested bonds force constants in Gaussian output file. I searched the freq-output file of my project and just found this string "Internal Coordinate...

06 June 2014 8,243 10 View

How should I treat the peptide with the cells?

The following is written in the article below: (A) Cancer cells in 6-well plates were treated with mouse pept ( 2 mM), human peptide (4 mM) or control peptide (4 mM) in a medium containing 2% FBS...

06 June 2014 2,536 7 View

Can anyone help with modelling a hetero dimer using modeler?

I have a complex, a receptor, and a ligand. The ligand is a short peptide. I want to make a model of the complex using a modeler program. How should I make the aln.file? I used the online...

06 June 2014 6,731 1 View

Can anyone help regarding insulin as a growth supplement for culturing HS578T cell line?

I don't have access to bovine insulin which used add the protocol of cell culture. I want to use human insulin for the culture so I have three question: first, has anyone used human insulin for...

05 May 2014 4,055 7 View

Does anyone know how I should find the exact value of force constant for a special bond or angle in a Gaussian Freq output file?

I performed a Gaussian optimization and frequency calculation on my molecule. The freq output file has lots of information and I don't know how I should find the exact value of the special bond?

01 January 2014 5,796 1 View