About project

This project as a course work was created to show pairwise distances between protein structures. The information about protein is taken from PDB(Protein Data Bank). This project provides basic visual perception of known protein structures throught website

How to start?

• First and foremost, you should install git + node JS + IDE for project

• Clone this repository: git clone https://github.com/SharpDevOps10/Protein-Visualization.Coursework

• Install dependencies : npm install

• Run this project : npm start

Usage

You can choose some protein structures, for instance :

• Beta hairpin
• Trp-cage
• Deoxyhemoglobin

Thus, you will see aminoacid structure of the particular protein. For example, for Beta hairpin it can be : Serine, Tryptophan, Threonine... etc

Information

As I've mentioned this project takes the information about the structure from PDB.

There are some links that were used in this coursework :

• The information about Identifiers in PDB : https://www.rcsb.org/docs/general-help/identifiers-in-pdb#small-molecule-instance-id
• The ATOM records present the atomic coordinates for standard amino acids and nucleotides : https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf (page 187)
• A typical PDB file describing a protein from Wiki : https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)

You can also look for information about mentioned proteins :

• Beta hairpin - https://en.wikipedia.org/wiki/Beta_hairpin
• Trp-cage - https://www.pnas.org/doi/10.1073/pnas.2233312100
• Deoxyhemoglobin - https://en.wikipedia.org/wiki/Hemoglobin

You can see an example of ATOM Record Format (Page 189)

Contacts

If you find any mistake, problem or bug in this project, please contact me : https://t.me/DanioRerio8

License

In my course work I used MIT License