Bioinformatics - Assignment #3 (Week 3)

 Hello,

Today I familiarized myself with iTASSER, which is a platform that uses algorithms to construct models of specific proteins that are being investigated. The protein I requested a model of belonged to Deinococcus Radiodurans, D. rad, and had the following locus tag Ga0133345_1136. Below are four images of the protein rotating through space.  






Comments

  1. KaylynnSeptember 25, 2020 at 9:47 AM

    Hello Anthony,

    Do you have any iTASSER results besides the images.

    ReplyDelete

Post a Comment

Popular posts from this blog

Bioinformatics- Assignment 8| UCSC Genome Browser

Image
Assignment 8 had me get acquainted with the UCSC genome browser, which is saturated with all different kinds of genomic information. I looked up my protein AMY1B and explored its genetic sequence along with some other loci on the same chromosome. That being said, when I filtered what was displayed in the data track to "NCBI RefSeq" my data track shrunk significantly, only displaying one gene body. When I clicked on the gene body it took me to a new window that listed the specifics of the gene that I had already read about in previous databases used. Taking note of this, it showed me how meticulous these databases strive to be in putting out information. Below is the best image I could get of the initial data track displayed in the UCSC genome browser. 
Read more

Bioinformatics - Assignment #1 (Week 1)

09/09/2020 Anthony Luna Today I finished the first assignment of the bioinformatics project focusing on proteins .  My assigned protein is Q5T084 AMY1B , also known as alpha-amylase 1B polypeptide (Reactome.org). It is found in Homo sapiens and aids in the bodily function of digestion and absorption. Specifically, digestion and absorption of branched starch, amylopectin, and linear starch, amylose (Reactome.org). All of which takes place in the extracellular region of various cells. Moving onto the size, mass, and structure of alpha-amylase 1B. The protein alpha-amylase is folded into three distinct domains, A, B, and C. Yet, my primary focus is on domain B, which has a length of 105 amino acids, aa, and a mass of 12.4 kilo Daltons, kDa (Proteinatlas.org). Alpha-amylase 1B is described as projecting off of domain A in a loop like fashion. However, when a calcium ion binds to domain B, it is then described as relatively rigid (Schutte) . As for diseases involving alpha-amylase 1B, ...
Read more