{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T22:50:33Z","timestamp":1792104633275,"version":"4.4.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62502334"],"award-info":[{"award-number":["62502334"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62506255"],"award-info":[{"award-number":["62506255"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62672153"],"award-info":[{"award-number":["62672153"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Pocket-conditioned molecular generation incorporates the three-dimensional (3D) geometry and chemical environment of protein binding sites into molecular design. However, receptor conformational variation can introduce distribution shifts between training and inference, particularly under cross-docking conditions. Existing approaches often do not fully exploit the correspondence between related receptor conformations during training.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a structure-conditioned 3D molecular generation framework that combines pocket-level contrastive learning with reference-conformation feature fusion. Built on a stepwise constructive generative model, these training-stage components encourage stable pocket representations across related conformations while preserving single-pocket inference without requiring a reference conformation. Evaluation on CrossDocked2020 and three external datasets, ASB-E, DUD-E, and APObind, demonstrates improvements in generation success, structural validity, and docking-related performance, particularly under cross-dock evaluation. These results support improved robustness of pocket-conditioned molecular generation under receptor conformational variation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The source code and reproduction instructions are available at https:\/\/github.com\/LHHHHuan\/MTMGen. Pretrained models and an archival code snapshot are available at https:\/\/doi.org\/10.5281\/zenodo.21944857.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag740","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T11:40:51Z","timestamp":1790941251000},"source":"Crossref","is-referenced-by-count":0,"title":["Pocket contrastive learning and conformation fusion for robust structure-conditioned 3D molecular generation under receptor conformational variation"],"prefix":"10.1093","volume":"42","author":[{"given":"Huan","family":"Liu","sequence":"first","affiliation":[{"name":"College of Electronic and Information Engineering, Suzhou University of Science and Technology , Suzhou, 215009,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3438-9259","authenticated-orcid":false,"given":"Yijie","family":"Ding","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , Harbin, 150001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyi","family":"Guo","sequence":"additional","affiliation":[{"name":"Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong SAR,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5921-8707","authenticated-orcid":false,"given":"Hongjie","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Electronic and Information Engineering, Suzhou University of Science and Technology , Suzhou, 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