What is Primary, Secondary and Tertiary Structures of a Protein

More resources:

https://www.youtube.com/watch?v=hok2hyED9go

https://foldit.fandom.com/wiki/Protein_backbone#:~:text=Protein backbone is what holds,atoms%2C and a few hydrogens.

Multiple Sequence Alignment

source: https://en.wikipedia.org/wiki/Multiple_sequence_alignment

Aligns three or more sequences of protein and take into account - mutations, insertions, deletions etc. MSA provides important information about homology of proteins and is frequently used as an input feature for many machine learning models. Obtaining a MSA alignment for a given sequence is a computationally expensive.

How to find MSA for a sequence: Running MSA’s on a server:

• Clustal Omega: A new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
  • How to Use

Distance Map:

source: https://www.nature.com/articles/s41598-020-70181-0 42–47, 42–52, 42–62, and 42–67 are examples of local, short, medium, and long-range distances

Backbone and Sidechain Atoms:

Source : https://arxiv.org/pdf/2111.07786.pdf - protein is represented by a set of nodes where each node is an amino acid residue in the protein where each node is the 3D co-ordinates of alpha carbon of the residue.