{"id":971,"date":"2026-02-13T17:00:35","date_gmt":"2026-02-13T11:30:35","guid":{"rendered":"http:\/\/202.54.249.134\/BIC-NII\/?page_id=971"},"modified":"2026-02-13T17:00:35","modified_gmt":"2026-02-13T11:30:35","slug":"workshop-2026","status":"publish","type":"page","link":"http:\/\/202.54.249.134\/BIC-NII\/workshop-2026\/","title":{"rendered":"Workshop 2026"},"content":{"rendered":"\n

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

AlphaFold3<\/h4>\n\n\n\n

URL: https:\/\/alphafoldserver.com\/<\/a><\/p>\n\n\n\n

Monomer<\/td>Example 1<\/a><\/td>Example 2<\/a><\/td><\/tr>
Dimer<\/td>Example 1<\/a><\/td>Example 2<\/a><\/td><\/tr>
Protein + Ligand<\/td>Protein Sequence<\/a><\/td>Ligand: FAD<\/td><\/tr>
Protein + RNA<\/td>Sequences<\/a><\/td><\/td><\/tr>
Protein + DNA<\/td>Sequences<\/a><\/td><\/td><\/tr>
Protein + DNA + Ion<\/td>Sequences<\/a><\/td>Ion: Sodium<\/td><\/tr>
Protein + PTMs<\/td>You can play with example 1<\/td><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

ESMFold<\/h4>\n\n\n\n

URL: https:\/\/esmatlas.com\/resources?action=fold<\/a><\/p>\n\n\n\n

Monomer<\/td>Example 1<\/a><\/td>Example 2<\/a><\/td><\/tr>
Dimer\u2013 API and Web server do not support Dimer. But you may use
ESMFold ColabFold Portal<\/td>		https:\/\/colab.research.google.com\/github\/sokrypton\/ColabFold\/blob\/main\/ESMFold.ipynb<\/a><\/td>http:\/\/pdbi.nii.ac.in\/AF_ESM\/7awv_Dimer.fa<\/a>
[OR]
Run on local server<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

ESM – API<\/strong><\/p>\n\n\n\n

curl -X POST --data \"GAMADIGSMDVLEYFERLKNRELAFVLDDLQLSDMVTRRGFSVIPFDDFDLAREDHPPAFVLVTRLDYHGKLMQAWETAKGISSHLSLAKFDTSPKSVEYSLDQLLSMDFAETLKRRGDYYDSVASTNRMEVVTPGAVLTCDFGNEIEIANNDVEMQKGWLYSVAEFFETSVINLEADRSSYTLNGDLCFTGLIYLCNRPDLKERASATMDELMRMSTRGRNVVSFVDNQIVRMELGGVDMTATLRELIVGKEREGSSTEFAMGCVEYPLAQDWTINSVMNEGSHGIHVGVGMGKEIPHMDFIAKGAELRIAESSDA\" https:\/\/api.esmatlas.com\/foldSequence\/v1\/pdb\/ > 6zsv_Out.pdb<\/code><\/pre>\n\n\n\n
How to predict multiple structures using the script?<\/strong>
Demo fasta file – Multi_batch.fa<\/a>
Download Script – ESM_script.py<\/a>
Command: python ESM_script.py

# If biopython is not installed, you install it with “pip install biopython”.<\/p>\n\n\n\n
import requests\nfrom Bio import SeqIO\nimport os,sys\n# Define the ESMFold API endpoint\nESMFOLD_API_URL = \"https:\/\/api.esmfold.org\/v1\/predict\"\ninput = \"Multi_batch.fa\"\nfor i, record in enumerate(SeqIO.parse(input, \"fasta\"), start=1):\n    sequence_id = record.id\n    sequence = str(record.seq)\n    print(f\"Processing sequence {i}: ID = {sequence_id}\")\n    cmd = \"curl -X POST --data \"\"+sequence+\"\" https:\/\/api.esmatlas.com\/foldSequence\/v1\/pdb\/ > \"+sequence_id.replace(\"|\",\"_\")+\".pdb\"\n    #print(cmd)\n    os.system(cmd)<\/code><\/pre>\n\n\n\n
How to run ESMFold on the local machine?<\/strong><\/p>\n\n\n\n
Option 1:\nwget http:\/\/pdbi.nii.ac.in\/AF_ESM\/Script_ESM.sh<\/strong>\nwget http:\/\/pdbi.nii.ac.in\/AF_ESM\/ESM_dim_ex.fa\nsbatch Script_ESM.sh<\/strong>\n\n\nOption 2:\nmodule load esmfold\/1.0.3<\/strong>\nwget http:\/\/pdbi.nii.ac.in\/AF_ESM\/ESM_dim_ex.fa<\/strong>\n\n## Command for Dimer Structure prediction\nesm-fold -i ESM_dim_ex.fa<\/strong> -o output_folder -m \/opt\/apps\/esmfiles\/<\/strong><\/code><\/pre>\n\n\n\n
How to run AlphaFold3 with ligand in the local machine?<\/strong><\/p>\n\n\n\n
Option 1:
wget http:\/\/pdbi.nii.ac.in\/AF_ESM\/Script_AF3_Lig.sh
sbatch Script_AF3_Lig.sh<\/strong>

Option 2
module load AlphaFold\/AF3
mkdir AF3_Lig
cd AF3_Lig
cp \/apps\/run_alphafold.py .
wget http:\/\/pdbi.nii.ac.in\/AF_ESM\/AF3_input_test_wMSA.json
python run_alphafold.py --json_path AF3_input_test_wMSA.json --model_dir \/opt\/apps\/af3_model --db_dir \/opt\/apps\/AF3_DB --output_dir Output_AF3 --run_data_pipeline False<\/strong><\/pre>\n\n\n\n
Additional Links<\/strong>:
PAE Viewer – https:\/\/pae-viewer.uni-goettingen.de\/<\/a>
PyMOL Download Link – https:\/\/pymol.org\/#download<\/a>
PyMOL License – https:\/\/pymol.org\/ep\/<\/a>
PyMOL Tutorial – https:\/\/pymol.sourceforge.net\/newman\/userman.pdf<\/a>
Chimera – https:\/\/www.cgl.ucsf.edu\/chimera\/download.html<\/a>
<\/p>\n\n\n\n
Practice Files<\/strong> – Download<\/a> (Needed for tomorrow’s session)<\/p>\n\n\n\n
Further Reading – Comparison of Structure Prediction Methods and Comparison of AlphaFold2, AlphaFold3 and ESM Fold: Click here<\/strong><\/a><\/p>\n\n\n\n
More Details:-<\/p>\n\n\n\n
AlphaFold2<\/td>Article – https:\/\/doi.org\/10.1038\/s41586-021-03819-2<\/a>
GitHub Source Code – https:\/\/github.com\/google-deepmind\/alphafold<\/a><\/td><\/tr>
AlphaFold3<\/td>Article – https:\/\/doi.org\/10.1038\/s41586-024-07487-w<\/a>
GitHub Source Code – https:\/\/github.com\/google-deepmind\/alphafold3<\/a><\/td><\/tr>
ESMFold<\/td>Article – https:\/\/doi.org\/10.1126\/science.ade2574<\/a>
GitHub Source Code – https:\/\/github.com\/facebookresearch\/esm<\/a><\/td><\/tr>
RoseTTAFold<\/td>Article – https:\/\/doi.org\/10.1126\/science.abj8754<\/a>
GitHub Source Code – https:\/\/github.com\/RosettaCommons\/RoseTTAFold<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n
Download Programs for SSH\/SCP connection (Only for Windows Users)
PuTTY – Download<\/a>
WinSCP – Download<\/a><\/p>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
Hands-on session for protein structure prediction by AlphaFold3 and ESMFoldCourse Instructors: Dr. Sanjeet Kumar Mahtha, MK Bhan Postdoctoral FellowSureshkumar V, Research ScholarDr. Debasisa Mohanty, Director AlphaFold3 URL: https:\/\/alphafoldserver.com\/ Monomer Example 1 Example 2 Dimer Example 1 Example 2 Protein + Ligand Protein Sequence Ligand: FAD Protein + RNA Sequences Protein + DNA Sequences Protein +… Read More »Workshop 2026<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-971","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/pages\/971","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/comments?post=971"}],"version-history":[{"count":1,"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/pages\/971\/revisions"}],"predecessor-version":[{"id":972,"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/pages\/971\/revisions\/972"}],"wp:attachment":[{"href":"http:\/\/202.54.249.134\/BIC-NII\/wp-json\/wp\/v2\/media?parent=971"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}