{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T12:02:13Z","timestamp":1791201733689,"version":"4.2.0"},"reference-count":37,"publisher":"Wiley","issue":"26","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2026,10,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    We introduce commutative algebra machine learning for RNA (CAML\u2010RNA), a framework that combines bipartite persistent homology (PH) and persistent Stanley\u2013Reisner theory (PSRT) for predicting RNA\u2013small\u2010molecule binding affinities. RNA\u2013ligand interactions are represented as bipartite atom\u2010pair point clouds, enabling element\u2010specific (ES, 36 pairs, 4 RNA\u2009\u00d7\u20099 ligand elements) and category\u2010specific (CS, 36 pairs, 4 RNA structural categories\u2009\u00d7\u20099 ligand elements) Vietoris\u2013Rips filtrations that extract\n                    <jats:italic>\u03b2<\/jats:italic>\n                    <jats:sub>0<\/jats:sub>\n                    and\n                    <jats:italic>\u03b2<\/jats:italic>\n                    <jats:sub>1<\/jats:sub>\n                    Betti curves (PH features, 3888\u2010dim combined), supplemented by persistent\n                    <jats:italic>f<\/jats:italic>\n                    \u2010vectors and\n                    <jats:italic>h<\/jats:italic>\n                    \u2010vectors from a true bipartite distance filtration (PSRT features, 3744\u2010dim, following Suwayyid and Wei). Applied to a curated benchmark of 143 RNA\u2013ligand complexes spanning seven structurally distinct subtypes, CAML\u2010RNA achieves Pearson's\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.7283 (RMSE\u2009=\u20091.08\u2009\n                    <jats:italic>pK<\/jats:italic>\n                    <jats:sub>d<\/jats:sub>\n                    \u2009units) under leave\u2010one\u2010out cross\u2010validation and\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.6255 under nested 10\u2010fold cross\u2010validation (), outperforming AffiGrapher (\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.498), RLaffinity (\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.559), and RLASIF (\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.666, all LOO\u2010CV). A subtype\u2010aware feature selection strategy achieves\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.940 for aptamers and\n                    <jats:italic>R<\/jats:italic>\n                    \u2009=\u20090.771 for the riboswitch family.\n                  <\/jats:p>","DOI":"10.1002\/jcc.70511","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T02:19:28Z","timestamp":1790821168000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>CAML<\/scp>\n                    \u2010\n                    <scp>RNA<\/scp>\n                    : Commutative Algebra Machine Learning for\n                    <scp>RNA<\/scp>\n                    \u2013Ligand Binding Affinity Prediction"],"prefix":"10.1002","volume":"47","author":[{"given":"Stalin","family":"Arulsamy","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences Lovely Professional University  Phagwara Punjab India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yashwanth","family":"Krishna","sequence":"additional","affiliation":[{"name":"Independent Researcher  Manipal Karnataka India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajesh","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice, School of Pharmaceutical Sciences Lovely Professional University  Phagwara Punjab India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9009-1561","authenticated-orcid":false,"given":"Vanktesh","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences Lovely Professional University  Phagwara Punjab India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/35101544"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr0681546"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3681"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01145"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a003566"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.024"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/wrna.1477"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrd.2018.93"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2019.02.046"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5c00973"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci700134p"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1571"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10822\u2010026\u201000781\u2010x"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00798"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00605"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa921"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae002"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2025.108367"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.3934\/fods.2025009"},{"key":"e_1_2_11_21_1","volume-title":"Combinatorial 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