{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T05:27:05Z","timestamp":1786512425866,"version":"build-2736575974"},"reference-count":50,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T00:00:00Z","timestamp":1786320000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"France 2030","doi-asserted-by":"publisher","award":["ANR-18-IDEX-0001_GR-E"],"award-info":[{"award-number":["ANR-18-IDEX-0001_GR-E"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Region Reunion and European Union","award":["2023062"],"award-info":[{"award-number":["2023062"]}]},{"name":"Region Reunion and European Union","award":["345879"],"award-info":[{"award-number":["345879"]}]},{"name":"UKRI CDT in AI for Healthcare","award":["P\/S023283\/1"],"award-info":[{"award-number":["P\/S023283\/1"]}]},{"name":"European Union (EU) and Region Reunion"},{"name":"FONDECYT Iniciaci\u00f3n","award":["11250295"],"award-info":[{"award-number":["11250295"]}]},{"DOI":"10.13039\/501100019701","name":"Centre for Biotechnology and Bioengineering","doi-asserted-by":"crossref","award":["FB0001"],"award-info":[{"award-number":["FB0001"]}],"id":[{"id":"10.13039\/501100019701","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100019701","name":"Centre for Biotechnology and Bioengineering","doi-asserted-by":"crossref","award":["AFB240001"],"award-info":[{"award-number":["AFB240001"]}],"id":[{"id":"10.13039\/501100019701","id-type":"DOI","asserted-by":"crossref"}]},{"award":["FB0001"],"award-info":[{"award-number":["FB0001"]}],"id":[{"id":"https:\/\/ror.org\/0066thn33","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AFB240001"],"award-info":[{"award-number":["AFB240001"]}],"id":[{"id":"https:\/\/ror.org\/0066thn33","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["497207454"],"award-info":[{"award-number":["497207454"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"award":["497207454"],"award-info":[{"award-number":["497207454"]}],"id":[{"id":"https:\/\/ror.org\/018mejw64","id-type":"ROR","asserted-by":"publisher"}]},{"name":"EU COST Action","award":["CA21160"],"award-info":[{"award-number":["CA21160"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Although deep learning has transformed protein structure prediction, the controlled generation of functional and experimentally tractable protein structures remains a major challenge in structural bioinformatics. Diffusion models offer a versatile approach to generating protein backbones, motif-conditioned scaffolds, all-atom structures and biomolecular interaction geometries, while accommodating explicit structural and functional constraints. This review focuses on coordinate- and residue-frame-based diffusion approaches for generating protein structures, paying particular attention to geometric equivariance, conditioning strategies, all-atom modelling and interaction-aware design. We compare representative methods derived from RoseTTAFold, frame-diffusion architectures, and oriented-residue-cloud representations according to their molecular representation, generative objective, and validation strategy. We examine the criteria used to evaluate generated proteins, such as stereochemical quality, structural consistency, designability, novelty, diversity, computational efficiency, and experimental performance. Particular attention is given to the distinction between learned structural distributions and condition-dependent thermodynamic ensembles. Future progress will depend on the integration of generative models with molecular mechanics, conformational sampling, uncertainty estimation, free-energy methods, and experimental design\u2013build\u2013test\u2013learn cycles. Within this framework, diffusion models offer candidate generation and constraint satisfaction capabilities within broader protein engineering workflows.<\/jats:p>","DOI":"10.3390\/ijms27167151","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T10:23:50Z","timestamp":1786357430000},"page":"7151","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diffusion-Based Protein Structure Design: Geometric Modelling, Validation Strategies, and Thermodynamic Challenges"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-4680-0069","authenticated-orcid":false,"given":"Wenran","family":"Li","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 & Universit\u00e9 de la R\u00e9union, INSERM, EFS, BIGR U1134, DSIMB Bioinformatics Team, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8545-0371","authenticated-orcid":false,"given":"Xavier","family":"Cadet","sequence":"additional","affiliation":[{"name":"Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8369-5746","authenticated-orcid":false,"given":"David","family":"Medina-Ortiz","sequence":"additional","affiliation":[{"name":"Departamento de Ingenier\u00eda en Computaci\u00f3n, Universidad de Magallanes, Avenida Bulnes, Punta Arenas 01855, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0089-7156","authenticated-orcid":false,"given":"Mehdi D.","family":"Davari","sequence":"additional","affiliation":[{"name":"Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6642-2367","authenticated-orcid":false,"given":"Ramanathan","family":"Sowdhamini","sequence":"additional","affiliation":[{"name":"National Centre for Biological Science, TIFR, Bangalore 560065, India"},{"name":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India"},{"name":"Institute of Bioinformatics and Applied Biotechnology, Bangalore 560066, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7542-9061","authenticated-orcid":false,"given":"Miloud","family":"Bessafi","sequence":"additional","affiliation":[{"name":"ENERGYLab, EA 4079, Facult\u00e9 des Sciences et Technologies, Universit\u00e9 de La Reunion, 97490 Saint-Denis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1399-2729","authenticated-orcid":false,"given":"Cedric","family":"Damour","sequence":"additional","affiliation":[{"name":"ENERGYLab, EA 4079, Facult\u00e9 des Sciences et Technologies, Universit\u00e9 de La Reunion, 97490 Saint-Denis, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5693-5353","authenticated-orcid":false,"given":"Yu","family":"Li","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, Beijing Institute of Artificial Intelligence, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6030-5928","authenticated-orcid":false,"given":"Alain","family":"Miranville","sequence":"additional","affiliation":[{"name":"Laboratoire de Math\u00e9matiques Appliqu\u00e9es, University Le Havre Normandie, 76600 Le Havre, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7112-5626","authenticated-orcid":false,"given":"Alexandre G.","family":"de Brevern","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 & Universit\u00e9 de la R\u00e9union, INSERM, EFS, BIGR U1134, DSIMB Bioinformatics Team, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3568-9595","authenticated-orcid":false,"given":"Frederic","family":"Cadet","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 & Universit\u00e9 de la R\u00e9union, INSERM, EFS, BIGR U1134, DSIMB Bioinformatics Team, 75015 Paris, France"},{"name":"PEACCEL, AI for Biologics, 75013 Paris, 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