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THE PROF. M. VIJAYAN SCHOOL OF MACROMOLECULAR X-RAY CRYSTALLOGRAPHY AND PROTEIN STRUCTURE PREDICTION
The Second Edition

Hands-on session for protein structure prediction by AlphaFold3 and ESMFold
Course Instructors:
Sureshkumar V, Research Scholar
Dr. Sanjeet Kumar Mahtha, MK Bhan Postdoctoral Fellow
Dr. Debasisa Mohanty, Director

AlphaFold3

URL: https://alphafoldserver.com/

MonomerExample 1Example 2
DimerExample 1Example 2
Protein + LigandProtein SequenceLigand: FAD
Protein + RNASequences
Protein + DNASequences
Protein + DNA + IonSequencesIon: Sodium
Protein + PTMsYou can play with example 1

ESMFold

URL: https://esmatlas.com/resources?action=fold

MonomerExample 1Example 2
Dimer (Local ESMFold)Example 1Example 2

ESM – API

curl -X POST --data "MSSIQILSTTTIHAPNHPNDYSIDLTPWDLQYLTFGINQKGVLYHHPPNLDTTNQIQHLKQSLLSTLEYFHPLTGRLNVTNHEDNTVSYSVNCNNEGALFIHAEAKDISVGEILESTYLPVILYSFFPLNGVKNYQGTTKPLFAVQVTELIDGIFIGCAINHSVVDGTAFWYFINTWAKISKGDFEISPVPSFKRWFPDSVQPPIRFQFPKESQNDEEEKLCKPMFERLFHFSKENIAKLKSKANLEAGKTRISSLQAVFTHIWRAIVRSRSVDPQEELKFGIDIGVRPRLTPPRKNDYF" https://api.esmatlas.com/foldSequence/v1/pdb/ > Out.pdb

How to predict multiple structures using the script?
Demo fasta file – tmp.fasta
Download Script – script.py
Command: python script.py

import requests
from Bio import SeqIO
import os,sys
ESMFOLD_API_URL = "https://api.esmfold.org/v1/predict"
input = "tmp.fasta"
for i, record in enumerate(SeqIO.parse(input, "fasta"), start=1):
    sequence_id = record.id
    sequence = str(record.seq)
    print(f"Processing sequence {i}: ID = {sequence_id}")
    cmd = "curl -X POST --data \""+sequence+"\" https://api.esmatlas.com/foldSequence/v1/pdb/ > "+sequence_id.replace("|","_")+".pdb"
    #print(cmd)
    os.system(cmd)

How to run ESMFold on the local machine?

module load esmfold/1.0.3

## Command for Monomer Structure prediction
esm-fold -i monomer.fasta -o output_folder -m /home/tools/esmfiles/

## Command for Dimer Structure prediction
esm-fold -i dimer.fasta -o output_folder -m /home/tools/esmfiles/

Further Reading – Comparison of Structure Prediction Methods and Comparison of AlphaFold2, AlphaFold3 and ESM Fold: Click here

More Details:-

AlphaFold2Article – https://doi.org/10.1038/s41586-021-03819-2
GitHub Source Code – https://github.com/google-deepmind/alphafold
AlphaFold3Article – https://doi.org/10.1038/s41586-024-07487-w
GitHub Source Code – https://github.com/google-deepmind/alphafold3
ESMFoldArticle – https://doi.org/10.1126/science.ade2574
GitHub Source Code – https://github.com/facebookresearch/esm
RoseTTAFoldArticle – https://doi.org/10.1126/science.abj8754
GitHub Source Code – https://github.com/RosettaCommons/RoseTTAFold

Download Programs for SSH/SCP connection (Only for Windows Users)
PuTTY – Download
WinSCP – Download