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...

31 December 2018 6,167 7 View

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...

31 December 2018 509 3 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...

09 October 2018 9,737 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.

07 August 2018 1,708 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...

31 December 2017 6,538 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...

31 December 2017 7,116 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...

08 September 2017 179 4 View

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

08 September 2017 8,631 3 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?

06 July 2017 6,058 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

05 June 2017 5,911 2 View

What is the most Operating System (OS) which can be INSTALL on Tiny hard devices like Raspberry Pi (RPi) hardware ?

I'm targeting to deploy a mesh network and manually configure MANET routing protocols. I'm preparing scenarios, architectures, and hard devices needed to do that. Are there some step-by-step...

03 March 2021 1,931 5 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

Can we distinguish the type of free fluid inside the pelvic and abdominal cavities whether blood or serous fluid using the ultrasound?

during ultrasound examination of acute abdomen, sometimes we see free fluid , can we know the type of fluid ,whether blood or not , using ultrasound only? if yes , what are the sonographic...

01 March 2021 7,476 4 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

Is there an open source free software for text mining and sentiment analysis?

I am looking for a free software for text mining and sentiment analysis for my research on customer review mining (it involves calculating polarity of attributes,opinion oriented information...

25 February 2021 1,920 6 View

Which are the journals for free paper publication?

A bunch of flower for everybody. I would like to ask about the list of journals which we can publish our paper for free. Thanks in advance. Sincerely Walid

25 February 2021 9,790 3 View