{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T19:39:39Z","timestamp":1786995579882,"version":"build-2736575974"},"posted":{"date-parts":[[2026,8,14]]},"group-title":"Bioinformatics","reference-count":106,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01AI158753"],"award-info":[{"award-number":["R01AI158753"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM122480"],"award-info":[{"award-number":["R35GM122480"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM148356"],"award-info":[{"award-number":["R35GM148356"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["F-2250"],"award-info":[{"award-number":["F-2250"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["F-1654"],"award-info":[{"award-number":["F-1654"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["F-1515"],"award-info":[{"award-number":["F-1515"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["F-0018"],"award-info":[{"award-number":["F-0018"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["F-0046"],"award-info":[{"award-number":["F-0046"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Texas Biologics","award":["TXB-24-02"],"award-info":[{"award-number":["TXB-24-02"]}]},{"name":"University of Texas at Austin Portugal","award":["2022.15740.UTA"],"award-info":[{"award-number":["2022.15740.UTA"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,8,14]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Understanding how molecular structure encodes biological function remains a grand challenge in drug discovery. Here, we present PubCheF-1, a deep learning model that predicts literature-derived biological function directly from chemical structure. PubCheF-1 was trained on a dataset linking molecules to labels derived from the scientific articles in which they appear, a strategy that connects disparate compounds through the language used to describe their functionalities. When tasked with identifying inhibitors of \u03b2-lactamases, including enzymes considered largely refractory to inhibition, PubCheF-1 predicted structurally distinct compounds that collectively have activity against all \u03b2-lactamase classes. Furthermore, hit compounds directly bind the enzyme active site, restore antibiotic efficacy in multidrug-resistant high-priority pathogens, and demonstrate potent activity in animal infection models. Together, these findings establish that machine learning-based prediction of biological function derived from the language of scientific literature allows the identification of bioactive molecules at high hit rates, thereby accelerating therapeutic discovery.<\/jats:p>","DOI":"10.64898\/2026.08.09.743788","type":"posted-content","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T23:05:14Z","timestamp":1786748714000},"source":"Crossref","is-referenced-by-count":0,"title":["Learning from human and chemical languages to predict biological function"],"prefix":"10.64898","author":[{"given":"Clayton W.","family":"Kosonocky","sequence":"first","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikol","family":"Kade\u0159\u00e1bkov\u00e1","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kangsan","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayesha J.S.","family":"Mahmood","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Dunmyre","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip","family":"Woolley","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristi","family":"Xing","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"},{"name":"Department of Biological Sciences, Columbia University, New York, 10027, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Winkler","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomer","family":"Babu","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filip","family":"Kade\u0159\u00e1bek","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan L.","family":"Sessler","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric V.","family":"Anslyn","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8808-180X","authenticated-orcid":false,"given":"Edward M.","family":"Marcotte","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"},{"name":"Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78705, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Y. Jessie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6246-5338","authenticated-orcid":false,"given":"Andrew D.","family":"Ellington","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"},{"name":"Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78705, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7449-1151","authenticated-orcid":false,"given":"Despoina A.I.","family":"Mavridou","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, TX, USA"},{"name":"John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, 78712, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026081712150574000_2026.08.09.743788v1.1","doi-asserted-by":"crossref","unstructured":"Oliveira RI , Pereira TO , Abbasi M , Salvador JAR , Arrais JP (2025) Deep learning for small-molecule drug discovery: from molecular design to clinical translation. J. Pharm. Anal. 101533.","DOI":"10.1016\/j.jpha.2025.101533"},{"key":"2026081712150574000_2026.08.09.743788v1.2","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1039\/D4SC03921A","article-title":"A review of large language models and autonomous agents in chemistry","volume":"16","year":"2025","journal-title":"Chem. Sci"},{"key":"2026081712150574000_2026.08.09.743788v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.01.021"},{"key":"2026081712150574000_2026.08.09.743788v1.4","unstructured":"Corso G , St\u00e4rk HJ , Bowen , Barzilay R , Jaakkola T. DiffDock: diffusion steps, twists, and turns for molecular docking; 2023."},{"key":"2026081712150574000_2026.08.09.743788v1.5","doi-asserted-by":"crossref","unstructured":"Passaro S , Corso G , Wohlwend J , Reveiz M , Thaler S , et al. (2025) Boltz-2: Towards accurate and efficient binding affinity prediction. bioRxiv.","DOI":"10.1101\/2025.06.14.659707"},{"key":"2026081712150574000_2026.08.09.743788v1.6","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/s43588-024-00699-0","article-title":"The future of machine learning for small-molecule drug discovery will be driven by data","volume":"4","year":"2024","journal-title":"Nat. Comput. Sci"},{"key":"2026081712150574000_2026.08.09.743788v1.7","doi-asserted-by":"publisher","DOI":"10.1021\/ar500432k"},{"key":"2026081712150574000_2026.08.09.743788v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1033"},{"key":"2026081712150574000_2026.08.09.743788v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1004"},{"key":"2026081712150574000_2026.08.09.743788v1.10","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00049"},{"key":"2026081712150574000_2026.08.09.743788v1.11","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1039\/D4DD00011K","article-title":"Mining patents with large language models elucidates the chemical function landscape","volume":"3","year":"2024","journal-title":"Digit. Discov"},{"key":"2026081712150574000_2026.08.09.743788v1.12","unstructured":"OpenAI (2023) GPT-4 Technical Report. arXiv:2303.08774 arXiv:2303.08774."},{"key":"2026081712150574000_2026.08.09.743788v1.13","unstructured":"(2019) No time to wait: securing the future from drug-resistant infections - Report to the secretary-general of the United Nations. Intragency Coordination Group on Antimicrobial Resistance (IACG)."},{"key":"2026081712150574000_2026.08.09.743788v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(18)31117-6"},{"key":"2026081712150574000_2026.08.09.743788v1.15","doi-asserted-by":"crossref","unstructured":"Bush K , Bradford PA (2016) \u03b2-Lactams and \u03b2-lactamase inhibitors: an overview. Cold Spring Harb. Perspect. Med. 6.","DOI":"10.1101\/cshperspect.a025247"},{"key":"2026081712150574000_2026.08.09.743788v1.16","first-page":"33","article-title":"Are all \u03b2-lactams created equal?","volume":"101","year":"1996","journal-title":"Scand. J. Infect. Dis. Suppl"},{"key":"2026081712150574000_2026.08.09.743788v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(21)02724-0"},{"key":"2026081712150574000_2026.08.09.743788v1.18","doi-asserted-by":"publisher","DOI":"10.1093\/clinids\/24.Supplement_1.S19"},{"key":"2026081712150574000_2026.08.09.743788v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2006.05.005"},{"key":"2026081712150574000_2026.08.09.743788v1.20","doi-asserted-by":"crossref","unstructured":"Bush K (2018) Past and present perspectives on \u03b2-lactamases. Antimicrob. Agents Chemother. 62.","DOI":"10.1128\/AAC.01076-18"},{"key":"2026081712150574000_2026.08.09.743788v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2004.02.003"},{"key":"2026081712150574000_2026.08.09.743788v1.22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01374"},{"key":"2026081712150574000_2026.08.09.743788v1.23","doi-asserted-by":"publisher","DOI":"10.1080\/14756366.2017.1344235"},{"key":"2026081712150574000_2026.08.09.743788v1.24","doi-asserted-by":"crossref","unstructured":"Alarcia-Lacalle A , Canut-Blasco A , Solin\u00eds MA , Isla A , Rodr\u00edguez-Gasc\u00f3n A (2025) Clinical efficacy, safety and pharmacokinetics of novel \u03b2-lactam\/\u03b2-lactamase inhibitor combinations: a systematic review. JAC Antimicrob. Resist. 7.","DOI":"10.1093\/jacamr\/dlaf096"},{"key":"2026081712150574000_2026.08.09.743788v1.25","doi-asserted-by":"publisher","DOI":"10.1021\/jm701500e"},{"key":"2026081712150574000_2026.08.09.743788v1.26","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/s41579-019-0159-8","article-title":"Interplay between \u03b2-lactamases and new \u03b2-lactamase inhibitors","volume":"17","year":"2019","journal-title":"Nat. Rev. Microbiol"},{"key":"2026081712150574000_2026.08.09.743788v1.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2019.04.002"},{"key":"2026081712150574000_2026.08.09.743788v1.28","doi-asserted-by":"crossref","unstructured":"Boudza R , Bounou S , Segura-Garcia J , Moukadiri I , Maicas S (2026) Artificial intelligence as a catalyst for antimicrobial discovery: From predictive models to de novo design. Microorganisms 14.","DOI":"10.3390\/microorganisms14020394"},{"key":"2026081712150574000_2026.08.09.743788v1.29","doi-asserted-by":"crossref","unstructured":"Sanapalli BKR , Palit S , Deshpande A , Tokala R , Sigalapalli DK , et al. (2026) Artificial intelligence and the discovery of antibiotics: reinventing with opportunities, challenges, and clinical translation. Antibiotics 15.","DOI":"10.3390\/antibiotics15020233"},{"key":"2026081712150574000_2026.08.09.743788v1.30","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1007\/s10462-021-10058-4","article-title":"Machine learning in drug discovery: a review","volume":"55","year":"2022","journal-title":"Artif. Intell. Rev"},{"key":"2026081712150574000_2026.08.09.743788v1.31","doi-asserted-by":"crossref","first-page":"1755843","DOI":"10.3389\/fbinf.2026.1755843","article-title":"Artificial intelligence in drug discovery from advanced molecular representation to pipeline applications","volume":"6","year":"2026","journal-title":"Front. Bioinform"},{"key":"2026081712150574000_2026.08.09.743788v1.32","unstructured":"Ahmad W , Simon E , Chithrananda S , Grand G , Ramsundar B (2022) ChemBERTa-2: towards chemical foundation models. arXiv arXiv:2209.01712."},{"key":"2026081712150574000_2026.08.09.743788v1.33","doi-asserted-by":"publisher","DOI":"10.1021\/ci00057a005"},{"key":"2026081712150574000_2026.08.09.743788v1.34","unstructured":"Landrum G (2013) RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling.: https:\/\/www.rdkit.org."},{"key":"2026081712150574000_2026.08.09.743788v1.35","doi-asserted-by":"crossref","unstructured":"Lin T-Y , Goyal P , Girshick R , He K , Doll\u00e1r P (2017) Focal loss for dense object detection. arXiv arXiv:1708.02002","DOI":"10.1109\/ICCV.2017.324"},{"key":"2026081712150574000_2026.08.09.743788v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1055"},{"key":"2026081712150574000_2026.08.09.743788v1.37","first-page":"375","article-title":"Translation between molecules and natural language","volume":"2022","year":"2022","journal-title":"2022 Conference on Empirical Methods in Natural Language Processing, EMNLP"},{"key":"2026081712150574000_2026.08.09.743788v1.38","unstructured":"Gu J , Jiang X , Shi Z , Tan H , Zhai X , et al. (2024) A survey on LLM-as-a-judge. arXiv arXiv:2411.15594."},{"key":"2026081712150574000_2026.08.09.743788v1.39","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0977-x"},{"key":"2026081712150574000_2026.08.09.743788v1.40","doi-asserted-by":"crossref","unstructured":"Chefer H , Gur S , Wolf L . Transformer interpretability beyond attention visualization; 2021. In Proceedings of the IEEE\/CVF Conference on Computer Vision and Pattern Recognition. pp. 782\u2013791.","DOI":"10.1109\/CVPR46437.2021.00084"},{"key":"2026081712150574000_2026.08.09.743788v1.41","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00675"},{"key":"2026081712150574000_2026.08.09.743788v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06887-8"},{"key":"2026081712150574000_2026.08.09.743788v1.43","doi-asserted-by":"publisher","DOI":"10.1021\/jm901137j"},{"key":"2026081712150574000_2026.08.09.743788v1.44","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.200700139"},{"key":"2026081712150574000_2026.08.09.743788v1.45","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.34.11.2184"},{"key":"2026081712150574000_2026.08.09.743788v1.46","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1177\/2472555220979589","article-title":"Selecting approaches for hit identification and increasing options by building the efficient discovery of actionable chemical matter from DNA-encoded libraries","volume":"26","year":"2021","journal-title":"SLAS Discov"},{"key":"2026081712150574000_2026.08.09.743788v1.47","doi-asserted-by":"crossref","unstructured":"Garofalo B , Prati F , Buonfiglio R , Coletta I , D\u2019Atanasio N , et al. (2021) Discovery of novel chemical series of OXA-48 \u03b2-lactamase inhibitors by high-throughput screening. Pharmaceuticals 14.","DOI":"10.3390\/ph14070612"},{"key":"2026081712150574000_2026.08.09.743788v1.48","unstructured":"Minond D , Saldanha SA , Spicer T , Qin L , Mercer BA , et al. (2010) HTS assay for discovery of novel metallo-\u03b2 lactamase (MBL) inhibitors. MLP Probe Reports. Bethesda (MD)."},{"key":"2026081712150574000_2026.08.09.743788v1.49","doi-asserted-by":"publisher","DOI":"10.1021\/jm301916b"},{"key":"2026081712150574000_2026.08.09.743788v1.50","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01009-09"},{"key":"2026081712150574000_2026.08.09.743788v1.51","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/s44259-024-00051-6","article-title":"Antibiotic susceptibility testing using minimum inhibitory concentration (MIC) assays","volume":"2","year":"2024","journal-title":"NPJ Antimicrob. Resist"},{"key":"2026081712150574000_2026.08.09.743788v1.52","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.11.4760-4762.2005"},{"key":"2026081712150574000_2026.08.09.743788v1.53","doi-asserted-by":"crossref","first-page":"109026","DOI":"10.1016\/j.envres.2019.109026","article-title":"Nonlinear dose-time-response functions and health-protective exposure limits for inflammation-mediated diseases","volume":"182","year":"2020","journal-title":"Environ.. Res"},{"key":"2026081712150574000_2026.08.09.743788v1.54","doi-asserted-by":"crossref","unstructured":"Furniss RCD , Kaderabkova N , Barker D , Bernal P , Maslova E , et al. (2022) Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. eLife 11.","DOI":"10.7554\/eLife.59046"},{"key":"2026081712150574000_2026.08.09.743788v1.55","doi-asserted-by":"publisher","DOI":"10.1021\/bi700300u"},{"key":"2026081712150574000_2026.08.09.743788v1.56","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01485-07"},{"key":"2026081712150574000_2026.08.09.743788v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.155"},{"key":"2026081712150574000_2026.08.09.743788v1.58","doi-asserted-by":"crossref","unstructured":"Wang X , Yang Y , Gao Y , Niu X (2020) Discovery of the novel inhibitor against New Delhi Metallo-\u03b2-lactamase based on virtual screening and molecular modelling. Int. J. Mol. Sci. 21.","DOI":"10.3390\/ijms21103567"},{"key":"2026081712150574000_2026.08.09.743788v1.59","doi-asserted-by":"crossref","unstructured":"Hamrick JC , Docquier JD , Uehara T , Myers CL , Six DA , et al. (2020) VNRX-5133 (Taniborbactam), a broad-spectrum inhibitor of serine- and metallo-\u03b2-lactamases, restores activity of cefepime in Enterobacterales and Pseudomonas aeruginosa . Antimicrob. Agents Chemother. 64.","DOI":"10.1128\/AAC.01963-19"},{"key":"2026081712150574000_2026.08.09.743788v1.60","doi-asserted-by":"crossref","unstructured":"Hillyer T , Shin WS (2024) Meropenem\/vaborbactam - a mechanistic review for insight into future development of combinational therapies. Antibiotics 13.","DOI":"10.3390\/antibiotics13060472"},{"key":"2026081712150574000_2026.08.09.743788v1.61","doi-asserted-by":"publisher","DOI":"10.1021\/jm9009718"},{"key":"2026081712150574000_2026.08.09.743788v1.62","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1021\/jm049899b","article-title":"Synthesis and evaluation of oxazaborolidines for antibacterial activity against Streptococcus mutans","volume":"47","year":"2004","journal-title":"J. Med. Chem"},{"key":"2026081712150574000_2026.08.09.743788v1.63","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2012.11.068"},{"key":"2026081712150574000_2026.08.09.743788v1.64","doi-asserted-by":"publisher","DOI":"10.1021\/jm980343w"},{"key":"2026081712150574000_2026.08.09.743788v1.65","unstructured":"Ester M , Kriegel H-P , Sander J , Xu X . A density-based algorithm for discovering clusters in large spatial databases with noise; 1996. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining. pp. 226\u2013231."},{"key":"2026081712150574000_2026.08.09.743788v1.66","unstructured":"Liu Y , Ott M , Goyal N , Du J , Joshi M , et al. (2019) RoBERTa: A Robustly Optimized BERT pretraining Approach. arXiv arXiv:1907.11692."},{"key":"2026081712150574000_2026.08.09.743788v1.67","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.1021\/acs.jcim.6c00299","article-title":"Polypharmacology browser PPB3: a web-based deep learning tool for target prediction using ChEMBL data","volume":"66","year":"2026","journal-title":"J. Chem. Inf. Model"},{"key":"2026081712150574000_2026.08.09.743788v1.68","doi-asserted-by":"publisher","DOI":"10.1021\/ci050011h"},{"key":"2026081712150574000_2026.08.09.743788v1.69","doi-asserted-by":"crossref","unstructured":"Draszawka K , Szymanski J (2023) From scores to predictions in multi-label classification: neural thresholding strategies. Appl. Sci. 13.","DOI":"10.3390\/app13137591"},{"key":"2026081712150574000_2026.08.09.743788v1.70","doi-asserted-by":"crossref","unstructured":"Kaderabkova N , Furniss RCD , Maslova E , Potter KE , Eisaiankhongi L , et al. (2026) Antibiotic potentiation and inhibition of cross-resistance in pathogens associated with cystic fibrosis. eLife 12.","DOI":"10.7554\/eLife.91082.3"},{"key":"2026081712150574000_2026.08.09.743788v1.71","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01138-07"},{"key":"2026081712150574000_2026.08.09.743788v1.72","doi-asserted-by":"publisher","DOI":"10.1186\/1475-2859-11-56"},{"key":"2026081712150574000_2026.08.09.743788v1.73","unstructured":"Ausubel FM , Brent R , Kingston RE , Moore DD , Seidman JG , et al. (1989) Protein Expression. Current Protocols in Molecular Biology. New York: Wiley. pp. 16.11\u201316.18."},{"key":"2026081712150574000_2026.08.09.743788v1.74","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1107\/S2059798320003198","article-title":"Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling","volume":"76","year":"2020","journal-title":"Acta Crystallogr. D"},{"key":"2026081712150574000_2026.08.09.743788v1.75","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1107\/S2059798317016035","article-title":"CCP4i2: the new graphical user interface to the CCP4 program suite","volume":"74","year":"2018","journal-title":"Acta Crystallogr. D"},{"key":"2026081712150574000_2026.08.09.743788v1.76","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444910045749"},{"key":"2026081712150574000_2026.08.09.743788v1.77","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444913015308"},{"key":"2026081712150574000_2026.08.09.743788v1.78","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798317017235"},{"key":"2026081712150574000_2026.08.09.743788v1.79","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-024-07487-W"},{"key":"2026081712150574000_2026.08.09.743788v1.80","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889807021206"},{"key":"2026081712150574000_2026.08.09.743788v1.81","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909052925"},{"key":"2026081712150574000_2026.08.09.743788v1.82","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444904019158"},{"key":"2026081712150574000_2026.08.09.743788v1.83","doi-asserted-by":"publisher","DOI":"10.1107\/S2052252514009324"},{"key":"2026081712150574000_2026.08.09.743788v1.84","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889809008784"},{"key":"2026081712150574000_2026.08.09.743788v1.85","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3330"},{"key":"2026081712150574000_2026.08.09.743788v1.86","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00311"},{"key":"2026081712150574000_2026.08.09.743788v1.87","doi-asserted-by":"crossref","first-page":"19606","DOI":"10.1038\/s41598-022-24111-x","article-title":"Influence of tramadol on bacterial burden in the standard neutropenic thigh infection model","volume":"12","year":"2022","journal-title":"Sci. Rep"},{"key":"2026081712150574000_2026.08.09.743788v1.88","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-6-55"},{"key":"2026081712150574000_2026.08.09.743788v1.89","doi-asserted-by":"publisher","DOI":"10.1042\/bj2760269"},{"key":"2026081712150574000_2026.08.09.743788v1.90","doi-asserted-by":"crossref","unstructured":"Garsevanyan S , Barlow M (2023) The Klebsiella pneumoniae carbapenemase (KPC) \u03b2-lactamase has evolved in response to ceftazidime avibactam. Antibiotics 13.","DOI":"10.3390\/antibiotics13010040"},{"key":"2026081712150574000_2026.08.09.743788v1.91","doi-asserted-by":"publisher","DOI":"10.1080\/14656566.2019.1660772"},{"key":"2026081712150574000_2026.08.09.743788v1.92","doi-asserted-by":"publisher","DOI":"10.1111\/j.1749-6632.2012.06796.x"},{"key":"2026081712150574000_2026.08.09.743788v1.93","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01633-05"},{"key":"2026081712150574000_2026.08.09.743788v1.94","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/48.5.717"},{"key":"2026081712150574000_2026.08.09.743788v1.95","doi-asserted-by":"crossref","unstructured":"Kaderabkova N , Bharathwaj M , Furniss RCD , Gonzalez D , Palmer T , et al. (2022) The biogenesis of \u03b2-lactamase enzymes. Microbiology 168.","DOI":"10.1099\/mic.0.001217"},{"key":"2026081712150574000_2026.08.09.743788v1.96","doi-asserted-by":"crossref","unstructured":"Furniss RCD , Kaderabkova N , Barker D , Bernal P , Maslova E , et al. (2022) Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. eLife 11.","DOI":"10.7554\/eLife.59046"},{"key":"2026081712150574000_2026.08.09.743788v1.97","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15123-0"},{"key":"2026081712150574000_2026.08.09.743788v1.98","unstructured":"Hanahan D (1985) In: Glover DM , editor. DNA cloning: a Practical Approach: IRL Press, McLean, Virginia. pp. 109."},{"key":"2026081712150574000_2026.08.09.743788v1.99","doi-asserted-by":"publisher","DOI":"10.1128\/jb.172.11.6557-6567.1990"},{"key":"2026081712150574000_2026.08.09.743788v1.100","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(80)90283-1"},{"key":"2026081712150574000_2026.08.09.743788v1.101","doi-asserted-by":"publisher","DOI":"10.1111\/1469-0691.12318"},{"key":"2026081712150574000_2026.08.09.743788v1.102","doi-asserted-by":"publisher","DOI":"10.3201\/eid1809.120355"},{"key":"2026081712150574000_2026.08.09.743788v1.103","doi-asserted-by":"crossref","unstructured":"Emeraud C , Escaut L , Boucly A , Fortineau N , Bonnin RA , et al. (2019) Aztreonam plus clavulanate, tazobactam, or avibactam for treatment of infections caused by metallo-\u03b2-lactamase-producing Gram-negative bacteria. Antimicrob. Agents Chemother. 63.","DOI":"10.1128\/AAC.00010-19"},{"key":"2026081712150574000_2026.08.09.743788v1.104","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(91)90599-7"},{"key":"2026081712150574000_2026.08.09.743788v1.105","doi-asserted-by":"publisher","DOI":"10.1007\/BF00587591"},{"key":"2026081712150574000_2026.08.09.743788v1.106","doi-asserted-by":"publisher","DOI":"10.1021\/jm901137j"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.08.09.743788","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T19:15:18Z","timestamp":1786994118000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.08.09.743788"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,14]]},"references-count":106,"URL":"https:\/\/doi.org\/10.64898\/2026.08.09.743788","relation":{},"subject":[],"published":{"date-parts":[[2026,8,14]]},"subtype":"preprint"}}