ArticleNucleic acids research2026
DynaRepo: the repository of macromolecular conformational dynamics.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.Acta crystallographica. Section D, Structural biology · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Hybrid Approach to Protein-Protein Complex Affinity Prediction Based on Language Models and Molecular Dynamics.International journal of molecular sciences · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- MDCompress: better, faster compression of molecular dynamics simulation trajectories.Bioinformatics (Oxford, England) · 2026Article
- The 2026 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2026Article
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Authors and funding
4 authors.
Funding
Abstract
Proteins, RNA, and DNA are central to virtually all cellular processes, often assembling into macromolecular complexes to perform their functions. While these molecules are inherently dynamic, most methods for studying their mechanisms focus on static structures. Recent deep learning advances in protein structure prediction highlight the potential of data-driven approaches, yet dynamic behavior that is critical for interactions such as antibody-antigen recognition, intrinsically disordered proteins, and protein-nucleic acid binding, remains underexplored. To address this gap, we present DynaRepo, a repository of macromolecular conformational dynamics comprising $\sim$450 complexes and $\sim$270 single-chain proteins from PDBbind, the Structural Antibody Database (SAbDab), and benchmark sets. Each complex was simulated in triplicate for 500 ns, totaling $>$1100 $\mu$s of molecular dynamics data, with extensive pre-calculated analyses. DynaRepo provides a foundation for dynamics-aware deep learning frameworks and is freely available at: https://dynarepo.inria.fr/.
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Registered trials
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