How to build m-RNA secondary structure by using bioinformatics tools ? I need the structure in the pdb format?

RNA structure prediction

01 February 2018 3,909 0 View

Why we have to use Gd.HCl and Urea were used for unfolding studies of protein but not others?

why only these denaturants used why not others can anybody give explanation for this?

01 February 2017 6,569 0 View

How can i calculate free energy between prtein and ligand?

I have done molecular docking of one protein and ligand but i don't know how do i have to calculate free energy in between these two molecules? can you suggest anyone commands related to this?

11 December 2016 2,140 1 View

Plz any one hlep, another crystallisation condition is 40%MPD, 0.2 DIAMMONIUM PHOSPHATE possibility of salt or protein?

i am getting big crystals by increasing MPD from 40% to 60%, is the possibility of getting mpd crystals or they are protein crystals, those crystals are not well formed plz give suggestions.

11 December 2016 6,837 1 View

Gingkotoxin dissolving or preparation?

Please can any one suggest me preparation or how to dissolve gingkotoxin for my experiments?

09 October 2016 4,771 4 View

Protein Dimer modeling?

i have protein dimer sequences of chain A and B, how can i model these two sequences? i want to get as dimer. is there any software ? can you suggest?

09 October 2016 7,064 1 View

Molecular simulation and dynamics of DNA & Protein?

09 October 2016 1,111 0 View

Protein-ligand simulation?

08 September 2016 9,709 3 View

Molecular dynamics and simulation?

Basically how many nanoseconds we have to use for protein simulation? i used 20 ns for modeled structure, is it sufficient or shall i increase the time? can you suggest anyone?

08 September 2016 5,569 8 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 3 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View

Problem with ligating 2.8 kb insert into 8.5 kb plasmid?

I am trying to clone 2 copies of the same mammalian gene into the pSF-CMV-Ub-Puro Ascl (contains HindIII, KpnI and NheI cut sites) plasmid. This is what the final product is supposed to look like...

24 February 2021 6,310 3 View