What is Z Score of template alignment in protein folding?

01 June 2022 1 546 Report

When we compare structure of two proteins, their is the notion of Z Score.

"A Z-score is simply the comparison of an actual alignment score with the scores obtained on a set of random sequences by a Monte-Carlo process. Scores are calculated using the Smith & Waterman [SW81] algorithm." https://www.weizmann.ac.il/csb/faculty_pages/Sussman/pdb25sp10/abstracts/Comet.html

Basically, when you do a template alignment in preparation for homology modelling, you need to find the proper sequence alignment between your query sequence and the sequence embodied in the template structure. The z-score indicates whether there is indeed a significant similarity between the two sequences, which is a prerequisite for successful homology modelling.

Badges
Science topic

Similar topics
Filing

More Sabab Aosaf's questions See All

Which one is best method to calculate Actual evapotranspiration form temp data in humid region, Where in Dec- Mar Average Temp in (minus) ...??

I have long term data set for Tmax, Tmin and Tavg

10 December 2018 4,513 3 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

How to make a time series imputation benchmark ?

Hello ! In a work, I have to benchmark different algorithms to fill in missing values in time series. I insist on the fact that this is imputation and not forecasting. In my case, I have access...

24 February 2021 7,470 7 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

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

Can I use a protein-devoid condition as my negative control in ELISA?

Hello, I am running a sandwich-type ELISA where I am trying to inhibit a protein-protein interaction using small molecules. For each experiment, I determine my Z' (Z-prime) to determine the...

23 February 2021 7,429 1 View