| import streamlit as st | |
| import random | |
| import hashlib | |
| import py3Dmol | |
| import requests | |
| import io | |
| from Bio import PDB | |
| def generate_sequence_from_words(words, length): | |
| seed = ' '.join(words).encode('utf-8') | |
| random.seed(hashlib.md5(seed).hexdigest()) | |
| amino_acids = "ACDEFGHIKLMNPQRSTVWY" | |
| return ''.join(random.choice(amino_acids) for _ in range(length)) | |
| def predict_structure(sequence): | |
| url = "https://api.esmatlas.com/foldSequence/v1/pdb/" | |
| headers = {"Content-Type": "application/x-www-form-urlencoded"} | |
| data = {"sequence": sequence} | |
| response = requests.post(url, headers=headers, data=data, timeout=300) | |
| if response.status_code == 200: | |
| return response.text | |
| else: | |
| st.error(f"Error in structure prediction: {response.status_code} - {response.text}") | |
| return None | |
| def visualize_protein(pdb_string): | |
| view = py3Dmol.view(width=800, height=400) | |
| view.addModel(pdb_string, 'pdb') | |
| view.setStyle({'cartoon': {'color': 'spectrum'}}) | |
| view.zoomTo() | |
| return view | |
| st.title("Protein Sequence Generator and Structure Predictor") | |
| st.write("Enter three random words to seed your protein sequence:") | |
| word1 = st.text_input("Word 1") | |
| word2 = st.text_input("Word 2") | |
| word3 = st.text_input("Word 3") | |
| sequence_length = st.number_input("Enter desired sequence length", | |
| min_value=50, | |
| max_value=400, | |
| value=100, | |
| step=10) | |
| if st.button("Generate Sequence and Predict Structure"): | |
| if word1 and word2 and word3: | |
| words = [word1, word2, word3] | |
| sequence = generate_sequence_from_words(words, sequence_length) | |
| st.write(f"Generated sequence inspired by '{word1}', '{word2}', and '{word3}' with length '{sequence_length}':") | |
| st.code(sequence) | |
| st.header("Protein Structure Prediction") | |
| with st.spinner("Predicting protein structure... This may take a few minutes."): | |
| pdb_string = predict_structure(sequence) | |
| if pdb_string: | |
| view = visualize_protein(pdb_string) | |
| st_py3dmol = py3Dmol.show3d(view, width=800, height=400) | |
| st.components.v1.html(st_py3dmol.startjs, height=400) | |
| st.success("Structure prediction complete!") | |
| st.write("Note: This is a computational prediction and may not represent the actual biological structure.") | |
| else: | |
| st.error("Failed to predict structure. Please try again.") | |
| else: | |
| st.error("Please enter all three words.") | |
| st.markdown(""" | |
| ## What to do next: | |
| 1. Experiment with different seed words and sequence lengths. | |
| 2. Learn about how protein sequences relate to their predicted structures. | |
| 3. Remember that these are computational predictions and may not represent the actual biological structure. | |
| 4. For real protein structures, visit the [Protein Data Bank (PDB)](https://www.rcsb.org/). | |
| Enjoy exploring the world of protein sequences and predicted structures! | |
| """) |