Data for ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences
Dataset Description |
This repository contains data and model weights associated with the publication "ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences". It includes the datasets used for training and evaluating a dynamic contact prediction model, ESMDynamic, as well as a script for conversion and usage. |
Subject |
Life Sciences |
Keywords |
Computational biology; Structural biology; Molecular dynamics; Machine learning; Protein modeling; Bioinformatics; Biophysics; Artificial intelligence |
License |
CC BY |
Funder |
U.S. National Science Foundation (NSF)-Grant:MCB-1845606 |
Funder |
U.S. National Science Foundation (NSF)-Grant:CHE-2136142 |
Corresponding Creator |
Diwakar Shukla |
| Version | DOI | Comment | Publication Date |
|---|---|---|---|
| 2 | 10.13012/B2IDB-3773897_V2 | Made substantial changes to the data after the peer review | 2026-04-17 |
| 1 | 10.13012/B2IDB-3773897_V1 | 2025-06-23 |
Files associated with this dataset are being processed for availability via Globus.
This is expected to complete within a few hours of publication.
Contact the Research Data Service
with any questions.
Contact the Research Data Service for help interpreting this log.
| Dataset | update: {"publication_state"=>["version candidate under curator review", "released"], "release_date"=>[nil, Fri, 17 Apr 2026]} | 2026-04-17T21:53:55Z |
| Dataset | update: {"version_comment"=>["The paper has been peer-reviewed for journal publication and substantial changes, including to the dataset, have been requested.", "Made substantial changes to the data after the peer review"]} | 2026-04-17T20:47:46Z |
| RelatedMaterial | update: {"note"=>[nil, ""]} | 2026-04-17T20:10:44Z |
| Dataset | update: {"hold_state"=>["version candidate under curator review", "none"]} | 2026-04-09T20:28:36Z |
| Dataset | update: {"version_comment"=>[nil, "The paper has been peer-reviewed for journal publication and substantial changes, including to the dataset, have been requested."]} | 2026-04-09T20:27:38Z |
| RelatedMaterial | create: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-3773897_V1", "uri"=>"10.13012/B2IDB-3773897_V1", "uri_type"=>"DOI", "citation"=>"Kleiman, Diego; Feng, Jiangyan; Xue, Zhengyuan; Shukla, Diwakar (2025): Data for ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-3773897_V1", "dataset_id"=>3391, "selected_type"=>"Dataset", "datacite_list"=>"IsNewVersionOf", "note"=>nil, "feature"=>nil} | 2026-04-09T20:26:21Z |
| RelatedMaterial | create: {"material_type"=>"Preprint", "availability"=>nil, "link"=>"https://doi.org/10.1101/2025.08.20.671365", "uri"=>"10.1101/2025.08.20.671365", "uri_type"=>"DOI", "citation"=>" Kleiman, D. E., Feng, J., Xue, Z. & Shukla, D. ESMDynamic: A Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences. (2025). doi:10.1101/2025.08.20.671365.", "dataset_id"=>3391, "selected_type"=>"Other", "datacite_list"=>"IsSupplementTo", "note"=>"", "feature"=>nil} | 2026-04-09T20:26:21Z |
| RelatedMaterial | create: {"material_type"=>"Code", "availability"=>nil, "link"=>"https://github.com/ShuklaGroup/esmdynamic", "uri"=>"https://github.com/ShuklaGroup/esmdynamic", "uri_type"=>"URL", "citation"=>"https://github.com/ShuklaGroup/esmdynamic", "dataset_id"=>3391, "selected_type"=>"Code", "datacite_list"=>"IsSupplementedBy", "note"=>"", "feature"=>nil} | 2026-04-09T20:26:21Z |
| Funder | create: {"name"=>"U.S. National Science Foundation (NSF)", "identifier"=>"10.13039/100000001", "identifier_scheme"=>"DOI", "grant"=>"CHE-2136142", "dataset_id"=>3391, "code"=>"NSF"} | 2026-04-09T20:26:21Z |
| Funder | create: {"name"=>"U.S. National Science Foundation (NSF)", "identifier"=>"10.13039/100000001", "identifier_scheme"=>"DOI", "grant"=>"MCB-1845606", "dataset_id"=>3391, "code"=>"NSF"} | 2026-04-09T20:26:21Z |
| Creator | create: {"family_name"=>"Shukla", "given_name"=>"Diwakar", "identifier"=>"0000-0003-4079-5381", "email"=>"diwakar@illinois.edu", "is_contact"=>true, "row_position"=>4} | 2026-04-09T20:26:21Z |
| Dataset | update: {"corresponding_creator_name"=>[nil, "Diwakar Shukla"], "corresponding_creator_email"=>[nil, "diwakar@illinois.edu"]} | 2026-04-09T20:26:21Z |
| Creator | create: {"family_name"=>"Xue", "given_name"=>"Zhengyuan", "identifier"=>"0009-0004-4738-4395", "email"=>"zxue8@illinois.edu", "is_contact"=>false, "row_position"=>3} | 2026-04-09T20:26:21Z |
| Creator | create: {"family_name"=>"Feng", "given_name"=>"Jiangyan", "identifier"=>"0000-0003-0292-6758", "email"=>"jyfeng20@gmail.com", "is_contact"=>false, "row_position"=>2} | 2026-04-09T20:26:21Z |
| Creator | create: {"family_name"=>"Kleiman", "given_name"=>"Diego", "identifier"=>"0000-0002-3833-5872", "email"=>"diegoek2@illinois.edu", "is_contact"=>false, "row_position"=>1} | 2026-04-09T20:26:21Z |