Bioinformatics (bif) Codes

Group Bioinformatics Assignments

Q3: Assignment: Protein Structure Prediction. Predict the 3D structure of a given protein sequence using homology modeling or threading techniques. Present the predicted protein structure along with an analysis of its potential functions and interactions. The answer demonstrates sequence-based prediction with ESMFold and saves the coordinates as a PDB file; ESMFold is a deep-learning alternative to template-based homology modeling.

Protein Structure Prediction

Solution and implementation for Q3 from Bioinformatics (bif).

3_protein_structure_workflow.py Download 
"""Predict and save a protein structure with the ESMFold API."""

import requests


sequence = input("Enter protein sequence: ").strip().upper()
response = requests.post(
    "https://api.esmatlas.com/foldSequence/v1/pdb/",
    data=sequence,
    timeout=120,
)
response.raise_for_status()

with open("predicted_structure.pdb", "w", encoding="utf-8") as file:
    file.write(response.text)

print("Predicted structure saved to predicted_structure.pdb")
print("View and validate the structure in PyMOL or another molecular viewer.")

Other Questions in Bioinformatics

See All Available Questions 


        

        

            

                Download