{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T08:51:38Z","timestamp":1775033498562,"version":"3.50.1"},"reference-count":65,"publisher":"American Chemical Society (ACS)","issue":"17","license":[{"start":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T00:00:00Z","timestamp":1724025600000},"content-version":"vor","delay-in-days":367,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000185","name":"Defense Advanced Research Projects Agency","doi-asserted-by":"publisher","award":["HR0011-19-2-0022"],"award-info":[{"award-number":["HR0011-19-2-0022"]}],"id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24-DK116204"],"award-info":[{"award-number":["U24-DK116204"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2023,9,11]]},"DOI":"10.1021\/acs.jcim.3c00347","type":"journal-article","created":{"date-parts":[[2023,8,18]],"date-time":"2023-08-18T18:26:08Z","timestamp":1692383168000},"page":"5457-5472","source":"Crossref","is-referenced-by-count":15,"title":["A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules"],"prefix":"10.1021","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4594-4577","authenticated-orcid":true,"given":"Changchang","family":"Liu","sequence":"first","affiliation":[{"name":"Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Kutchukian","sequence":"additional","affiliation":[{"name":"Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nhan D.","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed","family":"AlQuraishi","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University, New York, New York 10032, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3364-1838","authenticated-orcid":true,"given":"Peter K.","family":"Sorger","sequence":"additional","affiliation":[{"name":"Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2023,8,18]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tips.2019.09.002"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1075762"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","unstructured":"Moret, N.; Liu, C.; Gyori, B. M.; Bachman, J. A.; Steppi, A.; Hug, C.; Taujale, R.; Huang, L.C.; Berginski, M. E.; Gomez, S. M.; Kannan, N.; Sorger, P. K. A Resource for Exploring the Understudied Human Kinome for Research and Therapeutic Opportunities. 2020, Preprint.  bioRxiv. Subject area: Systems Biology. https:\/\/www.biorxiv.org\/content\/10.1101\/2020.04.02.022277v3 (accessed 2023-08-15),10.1101\/2020.04.02.022277.","DOI":"10.1101\/2020.04.02.022277"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(95)90405-0"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-17-2291"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1938"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2559"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2019.05.005"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.530"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1038\/nrd3600"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1328"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1068"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1358"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/bi062142x"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.36.040306.132550"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1007\/s12539-019-00327-w"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2020.03.003"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4233"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.03.004"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz111"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty593"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2008.11.009"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1038\/srep46710"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq112"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1021\/ci2003889"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.6b00610"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-04762-3"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.8b00507"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00650"},{"key":"ref30\/cit30","unstructured":"Ragoza, M.; Turner, L.; Koes, D. R. Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks. 2017, arXiv:1710.07400 [cs, q-bio, stat].  ArXiv Preprint. https:\/\/arxiv.org\/abs\/1710.07400 (accessed 2023-08-15)."},{"key":"ref31\/cit31","unstructured":"Thomas, N.; Smidt, T.; Kearnes, S.; Yang, L.; Li, L.; Kohlhoff, K.; Riley, P. Tensor Field Networks: Rotation- and Translation-Equivariant Neural Networks for 3D Point Clouds. May 18, 2018,  arXiv Preprint. http:\/\/arxiv.org\/abs\/1802.08219 (accessed 2022-06-11)."},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b00628"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1225"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00411"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1990"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2019.02.018"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/acs.accounts.6b00491"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2017.11.009"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004728"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv082"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2932-0"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1406"},{"key":"ref44\/cit44","unstructured":"Lee, D.H. Pseudo-Label: The Simple and Efficient Semi-Supervised Learning Method for Deep Neural Networks.  ICML 2013 Workshop: Challenges in Representation Learning (WREPL); 2013."},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty374"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c01184"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1021\/ci00057a005"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1002\/minf.201500010"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0220113"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","unstructured":"Paggi, J. M.; Belk, J. A.; Hollingsworth, S. A.; Villanueva, N.; Powers, A. S.; Clark, M. J.; Chemparathy, A. G.; Tynan, J. E.; Lau, T. K.; Sunahara, R. K.; Dror, R. O. Leveraging Non-Structural Data to Predict Structures of Protein\u2013Ligand Complexes. 2020, Preprint.  bioRxiv. Subject area: Biophysics. https:\/\/www.biorxiv.org\/content\/10.1101\/2020.06.01.128181v2 (accessed 2023-08-15),10.1101\/2020.06.01.128181.","DOI":"10.1101\/2020.06.01.128181"},{"key":"ref52\/cit52","unstructured":"Corso, G.; St\u00e4rk, H.; Jing, B.; Barzilay, R.; Jaakkola, T. DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. February 11, 2023,  arXiv Preprint. http:\/\/arxiv.org\/abs\/2210.01776 (accessed 2023-02-26)."},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2020.03.002"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01283-4"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23157-1"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.1c02159"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17437-5"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.3389\/fddsv.2021.728551"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"ref60\/cit60","unstructured":"Landrum, G. RDKit: Open-Source Cheminformatics; 2020. Http:\/\/Www.Rdkit.Org (accessed 2023-08-15)."},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0506s15"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr055"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-3-33"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1038\/srep01448"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki524"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c00347","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c00347","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T10:49:13Z","timestamp":1724064553000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.3c00347"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,18]]},"references-count":65,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2023,9,11]]}},"alternative-id":["10.1021\/acs.jcim.3c00347"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.3c00347","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,18]]}}}