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In silico methods for prescreening potential NR binders with predictive binding ability are highly desired for NR-related drug development but are rarely reported. Here, we present the PbsNRs (Predicting binders and scaffolds for Nuclear Receptors), a user-friendly web server designed to predict the potential NR binders and scaffolds through proteochemometric modeling. The utility of PbsNRs was systemically evaluated using both chemical compounds and natural products. Results indicated that PbsNRs achieved a good prediction performance for chemical compounds on internal (ROC-AUC\u2009=\u20090.906, where ROC is Receiver-Operating Characteristic curve and AUC is the Area Under the Curve) and external (ROC-AUC\u2009=\u20090.783) datasets, outperforming both compound\u2013ligand interaction tools and NR-specific predictors. PbsNRs also successfully identified bioactive chemical scaffolds for NRs by screening massive natural products. Moreover, the predicted bioactive and inactive natural products for NR2B1 were experimentally validated using biosensors. PbsNRs not only aids in screening potential therapeutic NR binders but also helps discover the essential molecular scaffold and guide the drug discovery for multiple NR-related diseases. The PbsNRs web server is available at http:\/\/pbsnrs.badd-cao.net.<\/jats:p>","DOI":"10.1093\/bib\/bbae710","type":"journal-article","created":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T00:29:47Z","timestamp":1736641787000},"source":"Crossref","is-referenced-by-count":0,"title":["PbsNRs: predict the potential binders and scaffolds for nuclear receptors"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5380-2435","authenticated-orcid":false,"given":"Genhui","family":"Zheng","sequence":"first","affiliation":[{"name":"Institute of Clinical Science, Zhongshan Hospital, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, School of Life Sciences, Fudan University , No. 180 Fenglin Road, Shanghai 200032 ,","place":["China"]},{"name":"Oden Institute for Computational Engineering and Sciences (ICES), University of Texas at Austin , No. 201 East 24th Street, Austin 78712, TX 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Shanghai Institute of Infectious Disease and Biosecurity, Intelligent Medicine Institute, School of Life Sciences, Fudan University , No. 180 Fenglin Road, Shanghai 200032 ,","place":["China"]},{"name":"Department of Mathematics and Statistics, McGill University , 805 Sherbrooke Street West, Montreal H3A 0B9, Quebec ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zikun","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Technology, Tongji University , No. 1239 Siping Road, Shanghai 200092 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8420-4593","authenticated-orcid":false,"given":"Jingxuan","family":"Qiu","sequence":"additional","affiliation":[{"name":"School of Health Science and Engineering, University of Shanghai for Science and Technology , No. 516 Jungong Road, Yangpu District, Shanghai 200093 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