{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T23:12:53Z","timestamp":1791846773485,"version":"4.3.4"},"reference-count":33,"publisher":"American Chemical Society (ACS)","issue":"13","license":[{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003246","name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["NWA-ORC 1292.19.272"],"award-info":[{"award-number":["NWA-ORC 1292.19.272"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2025,7,14]]},"DOI":"10.1021\/acs.jcim.5c00603","type":"journal-article","created":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T11:01:01Z","timestamp":1751281261000},"page":"7013-7023","source":"Crossref","is-referenced-by-count":20,"title":["Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9879-1004","authenticated-orcid":true,"given":"Linde","family":"Schoenmaker","sequence":"first","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enzo G.","family":"Sastrokarijo","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1381-8464","authenticated-orcid":true,"given":"Laura H.","family":"Heitman","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"},{"name":"Oncode Institute","place":["Leiden, The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joost B.","family":"Beltman","sequence":"additional","affiliation":[{"name":"Division of Cell Systems and Drug Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4951-9220","authenticated-orcid":true,"given":"Willem","family":"Jespers","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0717-1817","authenticated-orcid":true,"given":"Gerard J.P.","family":"van Westen","sequence":"additional","affiliation":[{"name":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-017-0232-0"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ddtec.2020.08.003"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr777"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1177\/02611929211029635"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061007"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00049"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2010.03.020"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1038\/nrd3954"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","unstructured":"Pentina, A.; Clevert, D.A. Multi-task proteochemometric modelling.\n                      ChemRxiv\n                      2022.10.26434\/chemrxiv-2022-d5tzd","DOI":"10.26434\/chemrxiv-2022-d5tzd"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","unstructured":"Seidl, P.; Vall, A.; Hochreiter, S.; Klambauer, G. Enhancing activity prediction models in drug discovery with the ability to understand human language.\n                      arXiv\n                      2023.10.48550\/arXiv.2303.03363","DOI":"10.48550\/arXiv.2303.03363"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c01180"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","unstructured":"Vinogradova, E.; Pats, K.; Moln\u00e1r, F.; Fazli, S. MLT-LE: predicting drug-target binding affinity with multi-task residual neural networks.\n                      arXiv\n                      2022.10.48550\/arXiv.2209.06274","DOI":"10.48550\/arXiv.2209.06274"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","unstructured":"Chan, L.; Verdonk, M.; Poelking, C. Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions.\n                      arXiv\n                      2023. 10.48550\/ARXIV.2308.09086.","DOI":"10.48550\/ARXIV.2308.09086"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","unstructured":"Devlin, J.; Chang, M.W.; Lee, K.; Toutanova, K. BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding. Preprint at http:\/\/arxiv.org\/abs\/1810.04805 2019.10.48550\/arXiv.1810.04805","DOI":"10.48550\/arXiv.1810.04805"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","unstructured":"Enevoldsen, K.;  MMTEB: Massive multilingual text embedding benchmark.\n                      arXiv\n                      2025.10.48550\/arXiv.2502.13595","DOI":"10.48550\/arXiv.2502.13595"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","unstructured":"Grootendorst, M. BERTopic: Neural topic modeling with a class-based TF-IDF procedure.\n                      arXiv\n                      2022.10.48550\/arXiv.2203.05794","DOI":"10.48550\/arXiv.2203.05794"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1004"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.4062\/biomolther.2011.19.1.001"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1111\/bph.13316"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-022-00672-x"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c00132"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz682"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","unstructured":"Li, Z.;  Towards general text embeddings with multi-stage contrastive learning.\n                      arXiv\n                      2023.10.48550\/arXiv.2308.03281","DOI":"10.48550\/arXiv.2308.03281"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","unstructured":"McInnes, L., Healy, J.; Melville, J. UMAP: Uniform manifold approximation and projection for dimension reduction.\n                      arXiv\n                      2018.10.48550\/arXiv.1802.03426","DOI":"10.48550\/arXiv.1802.03426"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00205"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-024-00908-y"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq313"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1021\/jm9700575"},{"key":"ref30\/cit30","first-page":"25422","volume":"35","author":"Iosipoi L.","year":"2022","journal-title":"Adv. Neural Inf. Process. Syst."},{"key":"ref31\/cit31","doi-asserted-by":"publisher","unstructured":"Zhang, D.;  ChemLLM: A chemical large language model.\n                      arXiv\n                      2024.10.48550\/arXiv.2402.06852","DOI":"10.48550\/arXiv.2402.06852"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1021\/jm300131x"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1042\/bj3510095"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c00603","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c00603","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T07:25:12Z","timestamp":1752909912000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c00603"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,30]]},"references-count":33,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2025,7,14]]}},"alternative-id":["10.1021\/acs.jcim.5c00603"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c00603","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2025-vnd2c","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,30]]}}}