protein-structure-prediction

Protein Structure Prediction

Overview

Protein structure prediction enables researchers to computationally determine the 3D conformation of proteins directly from their amino acid sequences. This skill covers AlphaFold2, ESMFold, RoseTTAFold, and ColabFold for structure prediction, alongside tools for quality assessment, structural alignment, and downstream analysis.

When to Use This Skill

• Predicting 3D structures of proteins with no experimental structure available
• Comparing predicted vs. experimental structures (PDB)
• Identifying binding sites and functional residues
• Modelling protein complexes (multimers) and protein-protein interactions
• Assessing model confidence using pLDDT scores and PAE maps
• Performing structural alignment and RMSD calculations
• Screening for druggable pockets in predicted structures

Quick Start

ESMFold (Fast, API-based)

import requests

def predict_structure_esmfold(sequence: str) -> str:
    """Predict structure via ESMFold API, returns PDB string."""
    response = requests.post(
        "https://api.esmatlas.com/foldSequence/v1/pdb/",
        headers={"Content-Type": "application/x-www-form-urlencoded"},
        data=sequence,
        timeout=120,
    )
    response.raise_for_status()
    return response.text

sequence = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL"

pdb_string = predict_structure_esmfold(sequence)
with open("predicted_structure.pdb", "w") as f:
    f.write(pdb_string)
print("Structure saved to predicted_structure.pdb")

ColabFold (AlphaFold2 via MSA server)

# Install ColabFold
pip install colabfold[alphafold]

# Run prediction (single sequence)
colabfold_batch input.fasta output_dir/ --num-recycle 3 --num-models 5