{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T16:30:43Z","timestamp":1778085043285,"version":"3.51.4"},"reference-count":41,"publisher":"American Chemical Society (ACS)","issue":"2","license":[{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100018625","name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission","doi-asserted-by":"publisher","award":["23S41900400"],"award-info":[{"award-number":["23S41900400"]}],"id":[{"id":"10.13039\/501100018625","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AI for Science Foundation of Fudan University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2025,1,27]]},"DOI":"10.1021\/acs.jcim.4c01373","type":"journal-article","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T02:32:31Z","timestamp":1736994751000},"page":"554-562","source":"Crossref","is-referenced-by-count":7,"title":["PPDock: Pocket Prediction-Based Protein\u2013Ligand Blind Docking"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-0181-4823","authenticated-orcid":true,"given":"Jie","family":"Du","sequence":"first","affiliation":[{"name":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China"},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1322-7530","authenticated-orcid":true,"given":"Mingzhi","family":"Yuan","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China"},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1937-6855","authenticated-orcid":true,"given":"Ao","family":"Shen","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China"},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9255-3897","authenticated-orcid":true,"given":"Manning","family":"Wang","sequence":"additional","affiliation":[{"name":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China"},{"name":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2025,1,15]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1021\/jm060999m"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2010.484460"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.3389\/fddsv.2022.969983"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.2174\/1386207321666180524110013"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1039\/D3SC05552C"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.1c02007"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1021\/acs.accounts.5b00516"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","unstructured":"Microsoft Research AI4Science and Microsoft Azure\nQuantum, The impact of large\nlanguage models on scientific discovery: a preliminary\nstudy using gpt-4.  arXiv 2023 preprint arXiv:2311.07361, 10.48550\/arXiv.2311.07361.","DOI":"10.48550\/arXiv.2311.07361"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90153-X"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0897"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.2174\/156802608786786624"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01982"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003571"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-021-00522-2"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1021\/ci300604z"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1021\/jm0306430"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref18\/cit18","unstructured":"Corso, G.; St\u00e4rk, H.; Jing, B.; Barzilay, R.; Jaakkola, T., DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. In  International Conference on Learning Representations (ICLR 2023), 2023."},{"key":"ref19\/cit19","volume":"36","author":"Pei Q.","year":"2024","journal-title":"Advances in Neural Information Processing Systems"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2021.09.007"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.3390\/molecules27144568"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.3390\/molecules200713384"},{"key":"ref23\/cit23","first-page":"9323","volume-title":"Proceedings of the 38th International conference on machine learning","author":"Satorras V. G.","year":"2021"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae455"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","unstructured":"Wallach, I.; Dzamba, M.; Heifets, A., AtomNet: a deep convolutional neural network for bioactivity prediction in structure-based drug discovery.  arXiv 2015 preprint arXiv:1510.02855 10.48550\/arXiv.1510.02855.","DOI":"10.48550\/arXiv.1510.02855"},{"key":"ref26\/cit26","doi-asserted-by":"crossref","unstructured":"Lu, W.; Wu, Q.; Zhang, J.; Rao, J.; Li, C.; Zheng, S., Tankbind: Trigonometry-aware neural networks for drug-protein binding structure prediction. In  Proceedings of the 36th International Conference on Neural Information Processing Systems 2022 (pp 7236\u20137249).","DOI":"10.1101\/2022.06.06.495043"},{"key":"ref27\/cit27","author":"Zhang Y.","journal-title":"Eleventh International Conference on Learning Representations"},{"key":"ref28\/cit28","first-page":"20503","volume-title":"Proceedings of the 39th International conference on machine learning","author":"St\u00e4rk H.","year":"2022"},{"key":"ref29\/cit29","unstructured":"Corso, G.; Deng, A.; Polizzi, N.; Barzilay, R.; Jaakkola, T. S., Deep Confident Steps to New Pockets: Strategies for Docking Generalization. In  The Twelfth International Conference on Learning Representations 2024."},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1021\/acs.accounts.6b00491"},{"issue":"31","key":"ref31\/cit31","first-page":"5281","volume":"8","author":"Landrum G.","year":"2013","journal-title":"Greg Landrum"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1126\/science.ade2574"},{"key":"ref33\/cit33","volume":"30","author":"Vaswani A.","year":"2017","journal-title":"Advances in neural information processing systems 30 (NIPS 2017)"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"ref35\/cit35","unstructured":"Qi, C. R.; Su, H.; Mo, K.; Guibas, L. J., Pointnet: Deep learning on point sets for 3d classification and segmentation. In  Proceedings of the IEEE conference on computer vision and pattern recognition 2017 (pp 652\u2013660)."},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv082"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-15571-7"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5b00654"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.8b11099"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.TM118.004156"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.9b04664"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01373","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c01373","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T09:14:41Z","timestamp":1737969281000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c01373"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,15]]},"references-count":41,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,1,27]]}},"alternative-id":["10.1021\/acs.jcim.4c01373"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.4c01373","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,15]]}}}