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

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

Metal incorporation in Autodock?

How do we have to incorporate metal in model structure of protein? is there any option in autodock? i want to do docking small ligand along with metal?

09 October 2016 9,319 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

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

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

What urea buffer can i use for biotagged protein extraction from streptavidin beads?

Hi all, I have been doing research on biotagged LDB1 proteins in Mel cells. I purify the proteins using M280 streptavidin beads. The yield is very low so I've been trying to optimize it by...

24 February 2021 5,749 3 View

Will SARS-CoV-2 Spike be broken into S1 and S2 by denaturing conditions?

Hello, I am performing a western blot of my SARS-CoV-2 Spike-pseudotyped lentiviral particles. I denature my virus by adding concentrated virus to 2X Laemmli buffer at 1:1, then boiling for...

17 February 2021 4,844 4 View

Kinetics of Enzyme production in Recombinant E Coli?

Hello, I am trying to find kinetic information (such as rate of enzyme production etc.) on the expression of taq polymerase in E-Coli after inserting a recombinant plasmid. Any help would be...

12 February 2021 1,386 3 View

Is it possible to quantify recombinant protein in the supernatant using SDS PAGE ?

I would like to quantify a recombinant protein (with native signal sequence) secreted by Pichia pastoris using the SDS PAGE. Since my standard protein (plant origin) is not pure, I would like to...

07 February 2021 3,880 9 View

How could a transcriptional factor purified as inclusion bodies (by using urea) exhibit a ratio 260/280>1?

I am working with a very unstable transcriptional factor. I use DNAse in the lysis buffer and I purify it as inclusion bodies, by using urea and 1M NaCl. After purification, I buffer exchange the...

05 February 2021 2,530 3 View

How to measure the concentration of a labeled protein with no tryptophan or tyrosines?

Hey I'm trying to measure the concentration of a protein I've purified and then labeled with Atto 647 flourescent dye. The protein has no tryptophans or tyrosines (although does have...

04 February 2021 4,482 4 View

How to prepare protein samples in EMSA assay?

Recently l was studying EMSA assay, but l didn't find any detailed information about protein sample. we can use two kinds of protein, including crude protein extracts and recombinant proteins. but...

02 February 2021 10,047 3 View

I'm interested to quantify Urea by HPLC method, reversed phase conditions are preferable. Is there a good method suited for urea?

I have to develop a method that can be good enough to run dozens of samples that include urea as the main compound. I prefer an HPLC method because of the convenience of running large numbers of...

01 February 2021 1,888 4 View