Nessa Pesaran Afsharian

12 Questions 9 Answers 0 Followers

Questions related from Nessa Pesaran Afsharian

I have problems with my SDS-PAGE results... I cant figure out the problem with my work. Is something wrong with my SDS run or protein samples?

Dear Scientists I ran my SDS-PAGE with 37.5 microliter protein + 12.5 microliter sample solvent in every well and with stacking gel with pH=6.8 and separating gel with pH=8.8 with 100 voltage for...

01 January 2019 595 3 View

How can a person see dots and positive result in dot blot but see no bands at western blot test?

Dear Scientists After protein expression, I did periplasmic and total protein extractions. I did the dot blot test to see if my proteins have been expressed. well, The dot blot result was perfect...

01 January 2019 6,254 7 View

Why does a protein protein complex fall apart during simulation with gromacs?

during a 200 ns simulation of a protein complex in water in the 150th nanosecond they fall apart. I have retrieved the complex from PDB. I wonder whether someone can help me with that should I...

10 October 2018 9,851 6 View

What is the best way to calculate protein-protein binding affinity and protein-protein binding free energy using gromacs?

Dear researchers I wonder whether you could help me with that question.

08 August 2018 1,775 1 View

should i remove the His Tag from my protein for surface plasmon resonance?

I am expressing my protein in E.coli expression system and to purify it I am gonna use His tag. After this i am going to use a method to measure the binding affinity between this protein and some...

01 January 2018 6,597 3 View

Will E.coli be able to express this protein?

Dear scientists I do have a mammalian protein which i want to express in E.coli.as we know one of the important factors in protein expression is the mRNA secondary structure. It's better for the...

01 January 2018 7,198 2 View

Hi.In simulating with gromacs should i simulate both monomers of a homodimer or one is enough?

I am using gromacs and the protein I use is a homodimer and both dimers bind from the same region to receptor, to calculate the free energy of binding do i need to use the dimer as input or the...

09 September 2017 248 4 View

What are the odds of 2 different binding energy calculation softwares (say foldx and gromacs) having the same result?

I have 10 mutants and foldx have told me mutant number 5 is the best, what are the odds of foldx choosing the same mutant as the best one?

09 September 2017 8,749 3 View

Hi.I wanna calculate the protein-protein binding free enenry with gromacs by MMPBSA where can i find a thorough step by step protocol for that?

I have found tons of complete step by step protocols for Amber.But i should do this with gromacs...but I can't for the life of me find a step by step (from A to Z ) tutorial for that...in...

08 August 2017 3,019 1 View

HI.How can i find a through protocol of process of the manufacture of an approved medicine?

Do the pharmaceutical companies publish a through protocol of the drug they sell?if yes how can we have access to them?

07 July 2017 6,114 5 View

Hi.How reliable can the haddock results be?

I am using haddock in my project ..but i don't know if my results are reliable or if the results from haddock can be easily published i wonder if someone could kindly help me

06 June 2017 5,975 2 View

Hi.i am working with haddock server and it keeps sending me error message which is written below what should i do?

Status: Out of sync (in children) Invalid members: ['p1', 'p2'] Member p1 (First molecule) : Out of sync (in children) Invalid members: ['r'] Member r (Restraint definition) : Out of sync...

01 January 2017 602 0 View