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Despite significant progress in protein structure prediction, approximating conformational ensembles under physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method\n                    <jats:italic>PETIMOT<\/jats:italic>\n                    (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank,\n                    <jats:italic>PETIMOT<\/jats:italic>\n                    shows superior performance in time and accuracy, capturing protein dynamics, particularly large\/slow conformational changes, compared with state-of-the-art diffusion and flow-matching approaches, as well as traditional physics-based models. Our code and protocols are available at https:\/\/github.com\/PhyloSofS-Team\/PETIMOT.\n                  <\/jats:p>","DOI":"10.1107\/s2059798326006054","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T12:07:21Z","timestamp":1783944441000},"page":"862-885","update-policy":"https:\/\/doi.org\/10.1107\/cm_01","source":"Crossref","is-referenced-by-count":1,"title":["<i>PETIMOT<\/i>\n                    : a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks"],"prefix":"10.1107","volume":"82","author":[{"given":"Valentin","family":"Lombard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien Nguyen","family":"Van","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1903-7220","authenticated-orcid":true,"given":"Sergei","family":"Grudinin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4870-6304","authenticated-orcid":true,"given":"Elodie","family":"Laine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"329","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"dez5002_bb1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"dez5002_bb2","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1038\/s41592-024-02272-z","volume":"21","author":"Ahdritz","year":"2024","journal-title":"Nat. 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