{"entity": "researcher", "timestamp": "2026-08-20T21:45:29.095Z", "family": "Chiu", "given": "Wah", "initials": "W", "orcid": "0000-0002-8910-3078", "affiliations": ["Biophysics Program, Stanford University School of Medicine, Stanford, California, USA.", "Department of Bioengineering and James Clark Center, Stanford University, Stanford, California, USA.", "Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.", "Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8267ae908be24f33911e05627d91cf2b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8267ae908be24f33911e05627d91cf2b"}}, "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", 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"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": "cda1c70fc46d4c869e2b7b707017c75d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cda1c70fc46d4c869e2b7b707017c75d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cda1c70fc46d4c869e2b7b707017c75d"}}, "title": "Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.", "authors": [{"family": "Kretsch", "given": "Rachael C", "initials": "RC", "orcid": "0000-0002-6935-518X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1f57ffede849e89b0d9d9bbc046357.json"}}, {"family": "Posani", "given": "Elisa", "initials": "E", "orcid": "0000-0002-0217-5125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b03be0680ce84690b76468cd39db87f3.json"}}, {"family": "Baulin", "given": "Eugene F", "initials": "EF", "orcid": "0000-0003-4694-9783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/130452384cc24bcf811776c67b7f4e5b.json"}}, {"family": "Bujnicki", "given": "Janusz M", "initials": "JM", "orcid": "0000-0002-6633-165X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/849faed3ae904eebba43069f225960bf.json"}}, {"family": "Bussi", "given": "Giovanni", "initials": "G", "orcid": "0000-0001-9216-5782", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c8dbc0071e143d1ac88198b4c3ee0a0.json"}}, {"family": "Cheatham", "given": "Thomas E", "initials": "TE", "orcid": "0000-0003-0298-3904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/191ef0fd576b45fdbea9846b09cbf247.json"}}, {"family": "Chen", "given": "Shi-Jie", "initials": "SJ", "orcid": "0000-0002-8093-7244", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c565c7327994283947d3b9fd5607e72.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Farsani", "given": "Masoud Amiri", "initials": "MA", "orcid": "0000-0001-5116-0483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b13d1b4e6593429ba11a6c8567387035.json"}}, {"family": "Fisher", "given": "Olivia N", "initials": "ON", "orcid": "0000-0002-0862-8367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb83e25f131a448e9b0a0bb20b4434b6.json"}}, {"family": "Gromiha", "given": "M Michael", "initials": "MM", "orcid": "0000-0002-1776-4096", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe21772caf004787b06cd70009216653.json"}}, {"family": "Gupta", "given": "Ayush", "initials": "A", "orcid": "0009-0006-1702-6946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa80553f16304670ac85fa328fcb4e2c.json"}}, {"family": "Hamada", "given": "Michiaki", "initials": "M", "orcid": "0000-0001-9466-1034", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/694d9ffc2a7f4d87ac7052395607ef9f.json"}}, {"family": "Harini", "given": "K", "initials": "K"}, {"family": "Hu", "given": "Gang", "initials": "G", "orcid": "0000-0002-7134-3380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/84adade1242a42e08d253f5d1571e30c.json"}}, {"family": "Huang", "given": "David", "initials": "D"}, {"family": "Iwakiri", "given": "Junichi", "initials": "J", "orcid": "0000-0002-4611-2142", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e2643f00e444ba3b5ad3ba7fcabb087.json"}}, {"family": "Jain", "given": "Anika", "initials": "A", "orcid": "0000-0002-0249-875X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f494cddb12c43c98da4b6e07d0bcdd9.json"}}, {"family": "Kagaya", "given": "Yuki", "initials": "Y", "orcid": "0000-0003-0146-1709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26d582bbf2644fa4a200aed015e0747a.json"}}, {"family": "Kihara", "given": "Daisuke", "initials": "D", "orcid": "0000-0003-4091-6614", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c1db8ff1b2e48be804c70a7241f272b.json"}}, {"family": "Kmiecik", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-7623-0935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7623e655b071405e89f199416a75fde2.json"}}, {"family": "Krishnan", "given": "Sowmya Ramaswamy", "initials": "SR", "orcid": "0000-0001-5404-3266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60ff1c2d34bc4d67b7bc60acf276c73e.json"}}, {"family": "Kurisaki", "given": "Ikuo", "initials": "I", "orcid": "0000-0003-4519-1093", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35b09db55e7444a0a48c50e25b665f56.json"}}, {"family": "Languin-Catto\u00ebn", "given": "Olivier", "initials": "O", "orcid": "0000-0002-0486-9841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8439f1f3719b45d6a261d73c12502d98.json"}}, {"family": "Li", "given": "Jun", "initials": "J", "orcid": "0000-0002-7011-1991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15115dfb13334392acad8fe4ce206d9b.json"}}, {"family": "Li", "given": "Shanshan", "initials": "S", "orcid": "0000-0002-7041-5960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72e0bf30413d43c3a223c9529ef7f467.json"}}, {"family": "Malekzadeh", "given": "Karim", "initials": "K", "orcid": "0009-0004-8185-4995", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/791099c9158042f495f944cc92ee4dfb.json"}}, {"family": "Nakamura", "given": "Tsukasa", "initials": "T", "orcid": "0000-0002-6312-3070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7320ac2ffa5d4d0faa5b3b18c4131020.json"}}, {"family": "Ni", "given": "Wentao", "initials": "W", "orcid": "0009-0002-7355-0073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94e07102442e4808a95b6e747ad99b46.json"}}, {"family": "Nithin", "given": "Chandran", "initials": "C", "orcid": "0000-0001-8212-6093", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/4014ca87f8a34c419bd36e37d077c959.json"}}, {"family": "Zhou", "given": "Yuanzhe", "initials": "Y", "orcid": "0000-0003-1858-3067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/272b5e82efe64e36b146bc49370afcca.json"}}, {"family": "Chiu", "given": "Wah", "initials": "W", "orcid": "0000-0002-8910-3078", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8267ae908be24f33911e05627d91cf2b.json"}}, {"family": "Case", "given": "David A", "initials": "DA", "orcid": "0000-0003-2314-2346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56a39a6d0c634346a5a1894de52a6a44.json"}}, {"family": "Das", "given": "Rhiju", "initials": "R", "orcid": "0000-0001-7497-0972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a568fabd21d43ff9721a349c4413745.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Proteins", "issn": "1097-0134", "volume": "94", "issue": "1", "pages": "381-402", "issn-l": "0887-3585"}, "abstract": "Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the Tetrahymena ribozyme at 2.2-2.3 \u00c5 resolution, collected through target R1260 in the CASP16 competition. Twenty-six groups participated in this solvation \"cryo-ensemble\" prediction challenge, submitting over 350 million atoms in total, offering the first opportunity to compare blind predictions of dynamic solvent shell ensembles to cryo-EM density. Predicted atomic ensembles were converted to density through local alignment and these densities were compared to the cryo-EM densities using Pearson correlation, Spearman correlation, mutual information, and precision-recall curves. These predictions show that an ensemble representation is able to capture information of transient or dynamic water and ions better than traditional atomic models, but there remains a large accuracy gap to the performance ceiling set by experimental uncertainty. Overall, molecular dynamics approaches best matched the cryo-EM density, with blind predictions from bussilab_plain_md, SoutheRNA, bussilab_replex, coogs2, and coogs3 outperforming the baseline molecular dynamics prediction. This study indicates that simulations of water and ions can be quantitatively evaluated with cryo-EM maps. We propose that further community-wide blind challenges can drive and evaluate progress in modeling water, ions, and other previously hidden components of biomolecular systems.", "doi": "10.1002/prot.70079", "pmid": "41204761", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2117461"}, {"db": "pmc", "key": "PMC13196887"}], "notes": [], "created": "2026-08-20T06:35:34.392Z", "modified": "2026-08-20T06:35:36.065Z"}, {"entity": "publication", "iuid": "463e3ac43dbe4134818b9a3c8e4f5a20", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/463e3ac43dbe4134818b9a3c8e4f5a20.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/463e3ac43dbe4134818b9a3c8e4f5a20"}}, "title": "Blind prediction of complex water and ion ensembles around RNA in CASP16.", "authors": [{"family": "Kretsch", "given": "Rachael C", "initials": "RC", "orcid": "0000-0002-6935-518X", "researcher": {"href": 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hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the Tetrahymena ribozyme at 2.2-2.3 \u00c5 resolution, collected through target R1260 in the CASP16 competition. 26 groups participated in this solvation 'cryo-ensemble' prediction challenge, submitting over 350 million atoms in total, offering the first opportunity to compare blind predictions of dynamic solvent shell ensembles to cryo-EM density. Predicted atomic ensembles were converted to density through local alignment and these densities were compared to the cryo-EM densities using Pearson correlation, Spearman correlation, mutual information, and precision-recall curves. These predictions show that an ensemble representation is able to capture information of transient or dynamic water and ions better than traditional atomic models, but there remains a large accuracy gap to the performance ceiling set by experimental uncertainty. Overall, molecular dynamics approaches best matched the cryo-EM density, with blind predictions from bussilab_plain_md, SoutheRNA, bussilab_replex, coogs2, and coogs3 outperforming the baseline molecular dynamics prediction. This study indicates that simulations of water and ions can be quantitatively evaluated with cryo-EM maps. We propose that further community-wide blind challenges can drive and evaluate progress in modeling water, ions and other previously hidden components of biomolecular systems.", "doi": "10.1101/2025.11.03.685595", "pmid": "41279659", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12637500"}, {"db": "pii", "key": "2025.11.03.685595"}], "notes": [], "created": "2026-08-20T11:07:31.471Z", "modified": "2026-08-20T11:07:31.803Z"}, {"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": 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"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"}]}