https://github.com/solrikk/biosynth
🔬 BioSynth is an innovative tool designed to simulate and visualize protein synthesis from DNA sequences. It integrates modern bioinformatics methods to provide a detailed understanding of the relationship between DNA sequences and their corresponding protein structures.
https://github.com/solrikk/biosynth
3d-visualization asyncio bioinformatics bioinformatics-tool biopython dna genetic-engineering genomics molecular-biology mutation protein-structure protein-synthesis py3dmol python rna
Last synced: 3 months ago
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🔬 BioSynth is an innovative tool designed to simulate and visualize protein synthesis from DNA sequences. It integrates modern bioinformatics methods to provide a detailed understanding of the relationship between DNA sequences and their corresponding protein structures.
- Host: GitHub
- URL: https://github.com/solrikk/biosynth
- Owner: Solrikk
- License: apache-2.0
- Created: 2024-07-07T16:12:48.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2024-07-11T12:51:48.000Z (11 months ago)
- Last Synced: 2025-02-03T12:17:02.869Z (4 months ago)
- Topics: 3d-visualization, asyncio, bioinformatics, bioinformatics-tool, biopython, dna, genetic-engineering, genomics, molecular-biology, mutation, protein-structure, protein-synthesis, py3dmol, python, rna
- Language: Python
- Homepage:
- Size: 400 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
-----------------
# BioSynth 🔬
_**BioSynth**_ is an innovative tool designed to simulate and visualize protein synthesis from DNA sequences. It integrates modern bioinformatics methods to provide a detailed understanding of the relationship between DNA sequences and their corresponding protein structures.
## Features ✨
- **🧬 DNA Transcription and Translation**: Converts DNA sequences into RNA sequences and subsequently translates them into protein sequences following the central dogma of molecular biology. [Learn more about Transcription and Translation](https://www.ncbi.nlm.nih.gov/books/NBK26887/).
- **🧪 Mutation Simulation**: Introduces random mutations in the DNA sequence to study their effects on the resulting protein. [Read about Mutation Types](https://en.wikipedia.org/wiki/Mutation).
- **🖼️ 3D Visualization**: Generates and visualizes 3D structures of proteins and DNA-protein complexes using py3Dmol. [Py3Dmol Documentation](https://3dmol.csb.pitt.edu/doc/).
- **⚡ Asynchronous Processing**: Utilizes Python's asyncio for efficient handling of multiple synthesis tasks concurrently. [Asyncio Official Documentation](https://docs.python.org/3/library/asyncio.html).
## How it Works
BioSynth performs several key steps to transform a DNA sequence into a visualized 3D modeled protein. In this section, we'll delve into each of these steps in detail:
### 1. 📝 Transcription
Transcription is the first step in protein synthesis, where the DNA sequence is transcribed into a messenger RNA (mRNA) sequence. This process involves replacing thymine (T) in the DNA with uracil (U) in the RNA.
- **Process**: The DNA sequence is unwound, and enzymes copy one of the strands to form mRNA.
- **Example**:
```python
dna_sequence = "ATGCGTACGTTAG"
rna_sequence = dna_sequence.replace("T", "U")
print("RNA Sequence:", rna_sequence)
```
2. **🔄 Translation**: The RNA sequence is then translated into a protein sequence based on codon tables. [A Guide to Translation](https://www.ncbi.nlm.nih.gov/books/NBK9849/).
3. **🧬 Protein Mutation**: A random base in the DNA sequence is mutated to simulate real-world genetic variations. [Understanding Genetic Mutations](https://www.genome.gov/Genetic-Disorders/What-are-Genetic-Mutations).
4. **🏗️ Structure Generation**: 3D structures of the synthesized protein and DNA-protein complexes are generated and saved as PDB files. [PDB File Format](https://www.rcsb.org/pages/help/format/pdbformat).
5. **🔍 Visualization**: The generated structures are visualized in an interactive 3D viewer. [3D Molecular Visualization Tools](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168215/).