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Although deep learning approaches have been widely explored for PPI modulator discovery, many rely on simplified representations that obscure interchain boundary information and fine-grained PPI\u2013modulator interaction (PPIMI) patterns, limiting their robustness under distribution shifts. To address this challenge, we introduce TvTPPIMI, a framework that leverages learnable boundary tokens to encode partner-aware boundary information and models PPIMI at atom\u2013residue resolution. In a case study targeting the AURKA\u2013TPX2 interaction, TvTPPIMI prioritized putative modulatory candidates from a small-molecule screening library. Structure-based docking, attention analysis, multireplica molecular dynamics simulations, MM\/GBSA binding free-energy estimation, and noncovalent interaction analyses provided post hoc physical support for the stable AURKA binding of selected candidates, highlighting CE02\u20136266 as the most favorable compound among the tested hits. Together, these results suggest that TvTPPIMI provides a generalizable computational framework with coarse-grained, attention-based interpretive cues for PPIMI prediction and can be integrated with structure- and dynamics-based analyses to support PPI modulator discovery.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c01921","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T06:00:58Z","timestamp":1788328858000},"page":"10806-10818","source":"Crossref","is-referenced-by-count":0,"title":["TvTPPIMI: A Boundary-Aware\nDual-View Framework for\nPredicting PPI-Modulator Interactions"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7898-1238","authenticated-orcid":true,"given":"Lan","family":"Yang","sequence":"first","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6510-1211","authenticated-orcid":true,"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"Suzhou University of Science and Technology , , ,","place":["Suzhou, China, 215009"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Tan","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furui","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongcheng","family":"Fang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajing","family":"Yuan","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4979-8242","authenticated-orcid":true,"given":"Heqi","family":"Sun","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. China, 200040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, P. R. 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China, 458030"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"issue":"9","key":"2026091409083516800_cit1","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1101\/gad.14.9.1027","article-title":"Protein\u2013Protein Interactions Define Specificity in Signal\nTransduction","volume":"14","author":"Pawson","year":"2000","journal-title":"Genes Dev."},{"issue":"2","key":"2026091409083516800_cit2","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network Biology:\nUnderstanding the Cell\u2019s Functional\nOrganization","volume":"5","author":"Baraba\u0301si","year":"2004","journal-title":"Nat. Rev. Genet."},{"issue":"7172","key":"2026091409083516800_cit3","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/nature06526","article-title":"Reaching\nfor High-Hanging Fruit in Drug Discovery at\nProtein\u2013Protein Interfaces","volume":"450","author":"Wells","year":"2007","journal-title":"Nature"},{"issue":"3","key":"2026091409083516800_cit4","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1038\/s41588-020-00774-y","article-title":"Comprehensive\nCharacterization Of\nProtein\u2013Protein Interactions Perturbed By Disease Mutations","volume":"53","author":"Cheng","year":"2021","journal-title":"Nat. Genet."},{"issue":"11","key":"2026091409083516800_cit5","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1038\/nrm1742","article-title":"What Is the Role of Protein Aggregation\nin Neurodegeneration?","volume":"6","author":"Ross","year":"2005","journal-title":"Nat. Rev. Mol. 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