Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

Where can I read the force field parameters of amino acids and protein ?

I am a beginner in the field of molecular dynamics and biochemistry. I need the parameters such as van der Waal radii, partial charge of each amino acid. How do I read directly the parameters from...

20 January 2021 3,541 3 View

What is the reference for the partial charges values for peptides shown in avagadro?

I built short peptides in Avagadro, using Build--->insert--->peptide. After constructing the short peptides of 4 amino acids(tetrapeptide). Under the drop-down, View--->Atomic...

27 December 2020 778 3 View

How to compute the Backward kinematics ?

I have been reading this paper. https://cnx.org/resources/9c9fe5128dfef772b498990a94c49df16c4f09ee/transformation_derivations.pdf Here, they have computed for forwarding kinematics to compute...

18 October 2020 8,208 3 View

How to plot the following XYZ coordinate file?

I am trying to plot the following points in VMD. It is plotting as points. However, It is not connecting the points from A to B to C to D to E to F to H by a line. How do I do it? If not in VMD,...

15 September 2020 4,282 3 View

What is the difference between TURN, COIL and BRIDGE in Protein structure?

I have been reading the following (open access) journal, In this paper, they have collected data samples from the loop region and categorically classified into TURN, COIL and BRIDGE, 3-10 helix...

10 September 2020 4,033 4 View

What could be the reason where i got some extra small peaks in my sample ?

Hi all, Actually, I have done the experiment where the single crystalline substrate has used to coat a thin film. In that, I have got substrate peaks and also thin-film material peaks also. But...

16 August 2020 6,532 11 View

How to design of PID controller using ANN?

27 March 2020 5,699 3 View

Hi, I would like to sense the Fe(III) in water, therefore how can I overcome the pH interference?

when adding the Fe compound in the water it gets deprotonated and from strong acid. 1.adding base leads to salt formation 2.adding buffer solution leads to Fe concentration change.

11 March 2020 1,785 3 View

What are the useful packages of i-vector/x-vector extraction in python?

Hi all, Recently, I have involved in the speaker language identification using i-vector /x-vector based approach. Kindly share any useful packages links in python to compile this research work....

04 February 2020 1,591 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

Can linear DNA be used as template for site-directed mutagenesis?

Is it possible to induce site-directed substitution mutation by quick-change method on linear dsDNA? or it has to be cloned in some vector? If yes, should it be treated with the Dpn1 enzyme...

03 March 2021 401 4 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

Which fluorescent dye to use for measuring total ROS production?

Is DCFDA appropriate for measuring total ROS production, or can it only detect certain types of ROS? If I want to measure total ROS production, which dye should I use?

01 March 2021 9,447 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

How long does it take to get a modeller(for homology modelling) license?

I submitted my e-mail address on modeller website to get a license. The problem is that, the site cannot process my school e-mail (ewhain.net). I submitted my Lab website and school name so that...

25 February 2021 9,054 3 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

Has anyone tried to scan fluorescence IHC slides with microarray scanner?

I have an old slide microarray scanner (VIDAR Revolution 4200) and would like to give it a "second life", as IHC scanner array (fluorescence dyes), FISH over tissue or similar. Has anyone tried...

24 February 2021 9,210 1 View

In what ways do fellow reaerchers think that mRNA vaccination may be under CRISPR systems technology application ?

There are many ways for mRNA to intervene with genome expression. This question is raised for experts in CRISPR systems. Any RNA does not stand alone within acell. There are many ways to become...

18 February 2021 9,109 5 View