CARpROT Viewer

CARpROT is an application written for the Motorola Science Cup 2023 competition.

Features

• Translates DNA and RNA to amino acids
• Finds proteins based on peptide chains
• Calculates properties of peptides:
  • Length
  • Chemical formula
  • Mass
  • Isoelectric Point
  • Charge
  • Extinction Coefficient
  • Hydrophobicity
• Displays protein features using RCSB Saguaro
• Displays 3D structure of proteins found in RCSB PDB
• Displays 2D skeletal structure of peptides requested form PepDraw

Technologies:

• React
• Typescript
• Electron

Libraries and APIs used:

• RCSB Search for protein identification
• RCSB Saguaro for displaying charts of protein features
• PepDraw for getting 2D images

Installation

• Download latest installer file (.exe) here
• Run installer
• After installation, start installed app

Development environment

Node.js is required to run the app

1. install dependencies

npm install

or

yarn install

2. run app

npm run dev

or

yarn dev

Usage

1. Click on the input button to open input drawer
2. Enter DNA/RNA sequence or import it from a file (drag it into input area, or use import button below it)
3. Click save
4. Choose a peptide from the list (you can filter out all non-protein peptides by using toggle switches)
5. If a selected peptide is a protein found in RCSB PDB a features chart and a 3D model will be displayed, otherwise only peptide properties and a 2D image will be displayed

How it works

1. DNA is translated to amino acids
2. From sequence of amino acids program selects substrings that start with 'M' (start) and end with '-' (end)
3. All found peptides are cross-checked with the RCSB PDB database for a matching protein
4. All peptides are displayed with option of filtering proteins found in the RCSB PDB
5. When a peptide is selected:
   1. Its properties are calculated
   2. An image from PepDraw is requested
   3. If the selected peptide is a protein:
      • A chart of its features is displayed
      • A 3D structure model is requested from RCSB PDB and displayed

Credits

Parts of logo designed by pch.vector and Bakar015 / Freepik