20 Questions 27 Answers 0 Followers
Questions related from Najme Dehghanbanadaki
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 476 8 View
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 303 3 View
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 1,715 4 View
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 8,728 1 View
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 6,781 0 View
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 5,291 3 View
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 9,818 2 View
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 424 4 View
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 3,322 1 View
Hi is there any instruction to refold Denileukin diftitox(ontak)? it is really vital for my project. every help is appreciate.
10 October 2015 5,005 0 View
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 4,419 1 View
We could set temperature with kinetic energy in MD. How about pressure in NPT phase?
01 January 2015 8,243 8 View
Is wnt3a overexpressed in pc3 cell lines? is there any helpfull article about expression profile of these cells?
09 September 2014 6,682 3 View
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 9,843 7 View
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 7,479 0 View
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 8,247 10 View
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 2,539 7 View
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 6,734 1 View
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 4,059 7 View
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 5,801 1 View
