https://github.com/d-k-deng/protein_optimize

A software tool designed for protein optimization, ProteinOpti integrates sequence manipulation with structural analysis, streamlining the generation, prediction, and evaluation of protein variants using Google Colab.
https://github.com/d-k-deng/protein_optimize

bioinformatics google-colab ipynb protein-sequences

Last synced: 2 months ago
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A software tool designed for protein optimization, ProteinOpti integrates sequence manipulation with structural analysis, streamlining the generation, prediction, and evaluation of protein variants using Google Colab.

• Host: GitHub
• URL: https://github.com/d-k-deng/protein_optimize
• Owner: D-K-Deng
• License: mit
• Created: 2023-09-30T15:44:04.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2023-11-05T17:26:40.000Z (about 1 year ago)
• Last Synced: 2024-10-11T15:40:13.815Z (2 months ago)
• Topics: bioinformatics, google-colab, ipynb, protein-sequences
• Language: Jupyter Notebook
• Homepage:
• Size: 1.1 MB
• Stars: 6
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Protein_Optimize

When trying to optimize protein designs, scientists usually want to try different places of residues replaced with specific residues, and they would like to get their properties. The primary impetus for designing the given code was to bridge the gap between sequence manipulation and structural analysis in protein optimization. Traditional methods often isolate these steps, requiring researchers to switch between multiple tools and platforms. The need was evident for an integrated solution that could:

  Generate sequence variants based on specific criteria：

  Predict the structure of these variants.

  Evaluate their properties to guide further optimization.

This code was envisioned as a one-stop solution to address these requirements, reducing protein optimization's complexity and time overhead.

This software tool allows users to simply use Google Colab and run online with simple sequence input to get multiple properties of the variant sequence. The current version allows users to modify the residues they would like to change, and it will automatically generate the variant sequence properties based on any-time replacement of the changing residues.