{"entity": "researcher", "timestamp": "2026-08-20T20:26:08.426Z", "family": "Marcia", "given": "Marco", "initials": "M", "orcid": "0000-0003-2430-0713", "affiliations": ["European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.", "Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.", "Istituto Italiano di Tecnologia, Genoa, Italy."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f"}}, "publications": [{"entity": "publication", "iuid": "11c546321bdd474bb28a7297c8f23c2f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/11c546321bdd474bb28a7297c8f23c2f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/11c546321bdd474bb28a7297c8f23c2f"}}, "title": "Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.", "authors": [{"family": "Kretsch", "given": "Rachael C", "initials": "RC", "orcid": "0000-0002-6935-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1f57ffede849e89b0d9d9bbc046357.json"}}, {"family": "Albrecht", "given": "Reinhard", "initials": "R"}, {"family": "Andersen", "given": "Ebbe S", "initials": "ES", "orcid": "0000-0002-6236-8164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51f81727aa324c44829d7c723ce257d6.json"}}, {"family": "Chen", "given": "Hsuan-Ai", "initials": "HA", "orcid": "0000-0002-0586-0742", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee4e13e7a5b454e9022ffa7680bcf51.json"}}, {"family": "Chiu", "given": "Wah", "initials": "W", "orcid": "0000-0002-8910-3078", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8267ae908be24f33911e05627d91cf2b.json"}}, {"family": "Das", "given": "Rhiju", "initials": "R", "orcid": "0000-0001-7497-0972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a568fabd21d43ff9721a349c4413745.json"}}, {"family": "Gezelle", "given": "Jeanine G", "initials": "JG", "orcid": "0000-0003-3664-6199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee1a5eefa5cc4899ad8e61d9510a2297.json"}}, {"family": "Hartmann", "given": "Marcus D", "initials": "MD", "orcid": "0000-0001-6937-5677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5015f301959b49f2a66bde477942bc1c.json"}}, {"family": "H\u00f6bartner", "given": "Claudia", "initials": "C", "orcid": "0000-0002-4548-2299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08d39678d8e547f98640daaa75a717db.json"}}, {"family": "Hu", "given": "Yimin", "initials": "Y", "orcid": "0000-0002-6965-8965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb96c578f3ca468baaa276de7006286a.json"}}, {"family": "Jadhav", "given": "Shekhar", "initials": "S", "orcid": "0009-0009-4682-7568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76d18bc7a67742b885d774cd31c144c8.json"}}, {"family": "Johnson", "given": "Philip E", "initials": "PE", "orcid": "0000-0002-5573-4891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81d25991af7d4fa7bdee266b89050310.json"}}, {"family": "Jones", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-7780-5278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73d004a420f347d1bfe888ce4898ca30.json"}}, {"family": "Koirala", "given": "Deepak", "initials": "D", "orcid": "0000-0001-6424-3173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5d4134954ce4e47aa8fca505f6a4111.json"}}, {"family": "Kristoffersen", "given": "Emil L", "initials": "EL", "orcid": "0000-0001-8965-8201", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/897ffe3502a849a99fb5b3d7a7dd3a8a.json"}}, {"family": "Largy", "given": "Eric", "initials": "E", "orcid": "0000-0002-6140-9788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c04ac7b4077f438a8d6e479f94aa7f26.json"}}, {"family": "Lewicka", "given": "Anna", "initials": "A", "orcid": "0000-0002-9578-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/327c1b62df5c498aa3c2d0029a1fdc22.json"}}, {"family": "Mackereth", "given": "Cameron D", "initials": "CD", "orcid": "0000-0002-0776-7947", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55a039b29bca4bf8b0f101938d99078f.json"}}, {"family": "Marcia", "given": "Marco", "initials": "M", "orcid": "0000-0003-2430-0713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f.json"}}, {"family": "Nigro", "given": "Michela", "initials": "M", "orcid": "0000-0003-1847-475X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a50b9c4b5640498f8686426279105d72.json"}}, {"family": "Ojha", "given": "Manju", "initials": "M", "orcid": "0009-0001-3907-431X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80feac208e104994a79819e472ce8f2c.json"}}, {"family": "Piccirilli", "given": "Joseph A", "initials": "JA", "orcid": "0000-0002-0541-6270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e84bbb8358bb49eab7555ecbca7c3b1f.json"}}, {"family": "Rice", "given": "Phoebe A", "initials": "PA", "orcid": "0000-0002-3467-341X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbfba5a48b1c4523a4fa514c19a8ec0a.json"}}, {"family": "Shin", "given": "Heewhan", "initials": "H", "orcid": "0000-0001-9656-6639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e50c905b06041b99a6e67fafe548a5f.json"}}, {"family": "Steckelberg", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0001-7988-9946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fcefc13ad0d45e3a4a97dd0acd39eeb.json"}}, {"family": "Su", "given": "Zhaoming", "initials": "Z", "orcid": "0000-0002-9279-1721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a78a004dc8445ad9898394f2f22cd84.json"}}, {"family": "Srivastava", "given": "Yoshita", "initials": "Y", "orcid": "0000-0001-9091-9851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/263d91d610a44205bdcfdea50647b998.json"}}, {"family": "Wang", "given": "Liu", "initials": "L", "orcid": "0000-0003-1243-9654", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02cbf036482942389c6842f0c923da3e.json"}}, {"family": "Wu", "given": "Yuan", "initials": "Y", "orcid": "0009-0000-6122-2457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ace6aa92a5ff4190a969c956e22fd7ae.json"}}, {"family": "Xie", "given": "Jiahao", "initials": "J", "orcid": "0000-0002-4632-2959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f0991beb8924034b10ed972e081c727.json"}}, {"family": "Zwergius", "given": "Nikolaj H", "initials": "NH", "orcid": "0009-0007-4155-2468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/635d9abc2c4f4c06ba0197a9cbfa2b92.json"}}, {"family": "Moult", "given": "John", "initials": "J", "orcid": "0000-0002-3012-2282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eecbcb5d519340c786c29125d8ee994d.json"}}, {"family": "Kryshtafovych", "given": "Andriy", "initials": "A", "orcid": "0000-0001-5066-7178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee89585cf7964096951cf7bd1b51ab95.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Proteins", "issn": "1097-0134", "volume": "94", "issue": "1", "pages": "51-78", "issn-l": "0887-3585"}, "abstract": "Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.", "doi": "10.1002/prot.70043", "pmid": "40905273", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2105475"}, {"db": "pmc", "key": "PMC12412911"}], "notes": [], "created": "2026-08-20T06:35:24.763Z", "modified": "2026-08-20T06:35:26.013Z"}, {"entity": "publication", "iuid": "45db34a7199043b8945865786f2c9f40", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45db34a7199043b8945865786f2c9f40.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45db34a7199043b8945865786f2c9f40"}}, "title": "Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.", "authors": [{"family": "Jadhav", "given": "Shekhar", "initials": "S"}, {"family": "Maiorca", "given": "Mauro", "initials": "M"}, {"family": "Manigrasso", "given": "Jacopo", "initials": "J", "orcid": "0000-0003-4076-8930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2897862f8e24315a7d88694d3595830.json"}}, {"family": "Saha", "given": "Spandan", "initials": "S", "orcid": "0009-0000-1090-4490", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a888f990acb14b049298d31eeb716d2a.json"}}, {"family": "Rakitch", "given": "Auriane", "initials": "A"}, {"family": "Muscat", "given": "Stefano", "initials": "S", "orcid": "0000-0002-2733-8357", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8c1e9739b0b48adbd877ebb2929cd30.json"}}, {"family": "Mulvaney", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4373-6160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ce33ebc4409457b94c20aa7b3f9b9aa.json"}}, {"family": "De Vivo", "given": "Marco", "initials": "M", "orcid": "0000-0003-4022-5661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/942bbfbb68d645128468a77681d1e8b5.json"}}, {"family": "Topf", "given": "Maya", "initials": "M", "orcid": "0000-0002-8185-1215", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833297a674b74861a3b829a1cf3e8153.json"}}, {"family": "Marcia", "given": "Marco", "initials": "M", "orcid": "0000-0003-2430-0713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f.json"}}], "type": "journal article", "published": "2025-11-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10195", "issn-l": "2041-1723"}, "abstract": "Many RNAs rely on their 3D structures for function. While acquiring functional 3D structures, certain RNAs form misfolded, non-functional states ('kinetic traps'). Instead, other RNAs sequentially assemble into their functional conformations over pre-folded scaffolds. Elucidating the principles of RNA sequential assembly is thus important to understand how RNAs avoid the formation of misfolded, non-functional states. Integrating single-particle electron cryomicroscopy (cryo-EM), image processing, in solution small-angle X-ray scattering (SAXS), EM-driven molecular dynamics (MD) simulations, structure-based mutagenesis, and enzymatic assays, we have visualized the sequential multidomain assembly of a self-splicing ribozyme of biomedical and bioengineering significance. Our work reveals a distinct dynamic interplay of helical subdomains in the ribozyme's 5'-terminal scaffold, which acts as a gate to control the docking of 3'-terminal domains. We identify specific conserved and functionally important secondary structure motifs as the key players for orchestrating the energetically inexpensive conformational changes that lead to the productive formation of the catalytic pocket. Our work provides a near-atomic resolution molecular movie of a large multidomain RNA assembling into its functionally active conformation and establishes a basis for understanding how RNA avoids the formation of non-functional 'kinetic traps'.", "doi": "10.1038/s41467-025-65502-8", "pmid": "41309593", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12660903"}, {"db": "pii", "key": "10.1038/s41467-025-65502-8"}], "notes": [], "created": "2026-08-20T08:54:14.047Z", "modified": "2026-08-20T08:54:14.312Z"}, {"entity": "publication", "iuid": "215688415d7e4696b8797ce839e549b4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/215688415d7e4696b8797ce839e549b4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/215688415d7e4696b8797ce839e549b4"}}, "title": "Conserved architecture of a functional lncRNA-protein interaction in the DNA damage response pathway", "authors": [{"family": "Assenza", "given": "Salvatore", "initials": "S", "orcid": "0000-0001-9983-8927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f486bace038c4a89b880fced4de03253.json"}}, {"family": "Blanco", "given": "Constanza", "initials": "C"}, {"family": "Favard", "given": "Cyril", "initials": "C", "orcid": "0000-0002-8304-2980", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2329e326dd80441b93071003f4a1ab1f.json"}}, {"family": "Carnesecchi", "given": "Julie", "initials": "J", "orcid": "0000-0002-3872-2215", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/972e025d45104821b75f97e6df54c3c9.json"}}, {"family": "Marcia", "given": "Marco", "initials": "M", "orcid": "0000-0003-2430-0713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f.json"}}, {"family": "Chill\u00f3n", "given": "Isabel", "initials": "I", "orcid": "0000-0002-3107-8738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43b54edc3b0f411aaba1b006695f9ac4.json"}}], "type": "posted-content", "published": "2025-07-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.07.24.666508", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:06:43.697Z", "modified": "2026-08-20T11:06:43.895Z"}, {"entity": "publication", "iuid": "caee923caabd4e12aee5a8c8ab3fafc1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/caee923caabd4e12aee5a8c8ab3fafc1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/caee923caabd4e12aee5a8c8ab3fafc1"}}, "title": "Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.", "authors": [{"family": "Kretsch", "given": "Rachael C", "initials": "RC", "orcid": "0000-0002-6935-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1f57ffede849e89b0d9d9bbc046357.json"}}, {"family": "Albrecht", "given": "Reinhard", "initials": "R"}, {"family": "Andersen", "given": "Ebbe S", "initials": "ES", "orcid": "0000-0002-6236-8164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51f81727aa324c44829d7c723ce257d6.json"}}, {"family": "Chen", "given": "Hsuan-Ai", "initials": "HA", "orcid": "0000-0002-0586-0742", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee4e13e7a5b454e9022ffa7680bcf51.json"}}, {"family": "Chiu", "given": "Wah", "initials": "W", "orcid": "0000-0002-8910-3078", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8267ae908be24f33911e05627d91cf2b.json"}}, {"family": "Das", "given": "Rhiju", "initials": "R", "orcid": "0000-0001-7497-0972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a568fabd21d43ff9721a349c4413745.json"}}, {"family": "Gezelle", "given": "Jeanine G", "initials": "JG", "orcid": "0000-0003-3664-6199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee1a5eefa5cc4899ad8e61d9510a2297.json"}}, {"family": "Hartmann", "given": "Marcus D", "initials": "MD", "orcid": "0000-0001-6937-5677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5015f301959b49f2a66bde477942bc1c.json"}}, {"family": "H\u00f6bartner", "given": "Claudia", "initials": "C", "orcid": "0000-0002-4548-2299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08d39678d8e547f98640daaa75a717db.json"}}, {"family": "Hu", "given": "Yimin", "initials": "Y", "orcid": "0000-0002-6965-8965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb96c578f3ca468baaa276de7006286a.json"}}, {"family": "Jadhav", "given": "Shekhar", "initials": "S", "orcid": "0009-0009-4682-7568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76d18bc7a67742b885d774cd31c144c8.json"}}, {"family": "Johnson", "given": "Philip E", "initials": "PE", "orcid": "0000-0002-5573-4891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81d25991af7d4fa7bdee266b89050310.json"}}, {"family": "Jones", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-7780-5278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73d004a420f347d1bfe888ce4898ca30.json"}}, {"family": "Koirala", "given": "Deepak", "initials": "D", "orcid": "0000-0001-6424-3173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5d4134954ce4e47aa8fca505f6a4111.json"}}, {"family": "Kristoffersen", "given": "Emil L", "initials": "EL", "orcid": "0000-0001-8965-8201", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/897ffe3502a849a99fb5b3d7a7dd3a8a.json"}}, {"family": "Largy", "given": "Eric", "initials": "E", "orcid": "0000-0002-6140-9788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c04ac7b4077f438a8d6e479f94aa7f26.json"}}, {"family": "Lewicka", "given": "Anna", "initials": "A", "orcid": "0000-0002-9578-2628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/327c1b62df5c498aa3c2d0029a1fdc22.json"}}, {"family": "Mackereth", "given": "Cameron D", "initials": "CD", "orcid": "0000-0002-0776-7947", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55a039b29bca4bf8b0f101938d99078f.json"}}, {"family": "Marcia", "given": "Marco", "initials": "M", "orcid": "0000-0003-2430-0713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/feedc9230e1949d7896f13f846cbe56f.json"}}, {"family": "Nigro", "given": "Michela", "initials": "M", "orcid": "0000-0003-1847-475X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a50b9c4b5640498f8686426279105d72.json"}}, {"family": "Ojha", "given": "Manju", "initials": "M", "orcid": "0009-0001-3907-431X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80feac208e104994a79819e472ce8f2c.json"}}, {"family": "Piccirilli", "given": "Joseph A", "initials": "JA", "orcid": "0000-0002-0541-6270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e84bbb8358bb49eab7555ecbca7c3b1f.json"}}, {"family": "Rice", "given": "Phoebe A", "initials": "PA", "orcid": "0000-0002-3467-341X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbfba5a48b1c4523a4fa514c19a8ec0a.json"}}, {"family": "Shin", "given": "Heewhan", "initials": "H", "orcid": "0000-0001-9656-6639", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e50c905b06041b99a6e67fafe548a5f.json"}}, {"family": "Steckelberg", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0001-7988-9946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fcefc13ad0d45e3a4a97dd0acd39eeb.json"}}, {"family": "Su", "given": "Zhaoming", "initials": "Z", "orcid": "0000-0002-9279-1721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a78a004dc8445ad9898394f2f22cd84.json"}}, {"family": "Srivastava", "given": "Yoshita", "initials": "Y", "orcid": "0000-0001-9091-9851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/263d91d610a44205bdcfdea50647b998.json"}}, {"family": "Wang", "given": "Liu", "initials": "L", "orcid": "0000-0003-1243-9654", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02cbf036482942389c6842f0c923da3e.json"}}, {"family": "Wu", "given": "Yuan", "initials": "Y", "orcid": "0009-0000-6122-2457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ace6aa92a5ff4190a969c956e22fd7ae.json"}}, {"family": "Xie", "given": "Jiahao", "initials": "J", "orcid": "0000-0002-4632-2959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f0991beb8924034b10ed972e081c727.json"}}, {"family": "Zwergius", "given": "Nikolaj H", "initials": "NH", "orcid": "0009-0007-4155-2468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/635d9abc2c4f4c06ba0197a9cbfa2b92.json"}}, {"family": "Moult", "given": "John", "initials": "J", "orcid": "0000-0002-3012-2282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eecbcb5d519340c786c29125d8ee994d.json"}}, {"family": "Kryshtafovych", "given": "Andriy", "initials": "A", "orcid": "0000-0001-5066-7178", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee89585cf7964096951cf7bd1b51ab95.json"}}], "type": "journal article", "published": "2025-04-18", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular. Here, we report quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs, however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, e.g., the nucleic-acid backbone bends or a base forms a non-standard hydrogen bond. These bends and non-canonical interactions are integral to form functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life-cycle, posing a future challenge for the community.", "doi": "10.1101/2025.04.15.649049", "pmid": "40568131", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12191101"}, {"db": "pii", "key": "2025.04.15.649049"}], "notes": [], "created": "2026-08-20T11:02:17.490Z", "modified": "2026-08-20T11:02:17.803Z"}]}