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

Can anyone please help me in processing SAR SLC data to generate interferogram using SNAP?

I have two scenes of the study area, one top and the other bottom. As per the tutorials and papers published, the step include coregistering the master sand slave images. However, when i try to...

24 February 2021 6,372 1 View

How to indicate the degree of litter decomposed by microbes?

Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...

23 February 2021 1,362 5 View

How to Implement Elastoplasticity in a PCL model in COMSOL Multiphysics?

I am using COMSOL Multiphysics 5.5. I am trying to simulate the tensile test of PCL scaffolds. However, regardless of the strain, I have the elastic region all the time which is not true when it...

23 February 2021 4,050 1 View

Model Volume fraction and magnetic field applications of nanofluids in ANSYS?

Hi I am working recently on a project where I have to study how the thermal properties or heat transfer enhancement of nanofluids as the volume fraction changes, or if a magnetic field is applied...

22 February 2021 961 2 View

How to model static fluids in ANSYS?

Hi I was wondering if there is a way of simulating static fluids (including brownian motion) of nanofluids in ANSYS. I am currently working on a theroretical based project where I am trying to...

20 February 2021 776 1 View

Would bisulfide sequencing result be affected if the tissue is fixed by perfusion?

I am looking into DNA methylation of mice as an aging marker along with other assays and recently I added brain IF to the list of assays. For this, I need to fix the brain by transcardial...

09 February 2021 9,012 3 View

Why E1g mode (Molybdenum disulfide) is undetectable in Raman spectroscopy?

I synthesized 1T/2H hybrid phase MoS2 on a graphite foil surface by hydrothermal method, and then analyzed it by Raman spectroscopy. As a result, three new peaks correspond to the 1T phase were...

04 February 2021 6,580 2 View

Can I use 500ng of DNA for restriction digestion?

The recommended amount of DNA for restriction digestion is 1ug in a 50ul rx I've got around 500-600ng of DNA in a total volume of 35ul. Would I get satisfactory results with this amount of DNA for...

31 January 2021 729 6 View

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View

How to show a protein is being dimerized in SDS-PAGE gel?

A protein dimerizes through CTD. I have expressed CTD of protein with two different tags. Now, I want to show that these CTD of protein dimerize in a pull-down assay. But my doubt is that if the...

29 January 2021 7,529 4 View

Problem with GST-fusion protein elution- Can anyone help?

18 December 2020 4,559 6 View

Why do protein and mRNA levels not always correlate with each other?

Hello, I have performed WB analysis and qPCR analysis to analyze the protein level and the rispective gene relative expression of mTOR, GBA1, LC3 genes in brain of mutant mice. I observed a...

01 December 2020 4,486 2 View

Infected plant protein lysate washing out purified GST-tagged protein on agarose resin?

Hi, I am trying to screen infected plant proteomes for targets of a secreted pathogen protein. I have purified the pathogen protein using a GST-tag on an agarose resin. I am using the Pierce...

23 November 2020 7,009 3 View

How can I confirm that a gene is downregulated in cancer cells through PCR?

A particular gene (gene A) is reported to be downregulated in cancer cells as compared to the normal cells. How can you prove this with the help of PCR?

27 September 2020 5,292 4 View

mRNA down-regulated but protein in Western Blot still there. Which is the most plausible explanation?

How is it possible that RT-qPCR demonstrate a down-regulation of my interested gene (from 22 to 27 ct) while WB is showing the protein expressed with the same intensity as in cells where the gene...

26 September 2020 2,860 15 View

How do I get rid of noise in my western blot?

02 September 2020 5,038 2 View

Can anyone help me in interpretation of RT PCR?

I have a gene X, it is an activator of different normal cellular pathways. If I use a control group, it should be highly expressive. And literature also defend this. I have use RT PCR, I use GAPDH...

06 August 2020 2,613 3 View

How do you report undetermined Ct values?

I have knocked down a gene of interest using siRNA and am using qRT-PCR to confirm reduced expression. All samples treated with non-specific siRNA have Ct values around 35, but all samples...

29 July 2020 8,198 3 View

Low mRNA expression versus High Protein expression?

I tested gene expression by RT PCR followed by Western blotting to test protein expression. I get an inverse correlation with several proteins (down-regulation at mRNA level and up-regulation...

09 June 2020 6,780 11 View