{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T16:09:17Z","timestamp":1788797357364,"version":"build-2803163510"},"reference-count":54,"publisher":"American Chemical Society (ACS)","issue":"13","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"High-Performance Cluster Computing Centre, HKBU internal funding","award":["RC-EMF\/23-24\/SCI\/01"],"award-info":[{"award-number":["RC-EMF\/23-24\/SCI\/01"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China (NSFC)","doi-asserted-by":"crossref","award":["22573087"],"award-info":[{"award-number":["22573087"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Multiscale molecular dynamics simulations that sequentially couple coarse-grained (CG) sampling with all-atom (AA) simulation are widely used to study biomolecular condensates, yet building such multiscale systems remains a practical challenge. Dense CG condensate configurations must be backmapped and converted into stable, explicitly solvated AA systems\u2500a step where severe steric clashes often prevent production simulation, creating a \u201crelaxation bottleneck\u201d. Here, we introduce CondenSimAdapter, a Python package that bridges this resolution gap by integrating SE(3)-transformer\u2013based cg2all backmapping with a physics-inspired optimization protocol (using Gaussian repulsion and soft-core potentials), which succeeds where standard energy minimization fails. CondenSimAdapter unifies four CG and nine AA force fields under a single interface. We validated the workflow by (1) demonstrating the robust elimination of major structure conflicts across diverse CG\u2013AA combinations, (2) verifying its functional versatility in preserving the structural integrity of multidomain proteins, and (3) confirming ensemble fidelity via a 2 \u03bcs atomistic simulation of a FUS LC condensate that accurately reproduced established macroscopic and microscopic properties. By resolving the dense-phase relaxation bottleneck and providing a highly accessible, streamlined workflow, CondenSimAdapter lowers the technical barrier to multiscale condensate simulations and enables systematic, high-throughput studies of protein phase separation. CondenSimAdapter is freely available at https:\/\/github.com\/hanlab-computChem\/CondenSimAdapter.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c00413","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T19:59:49Z","timestamp":1782849589000},"page":"7337-7344","source":"Crossref","is-referenced-by-count":0,"title":["CondenSimAdapter:\nA Versatile Builder for Multiscale\nSimulations of Protein Condensates with Broad Force-Field Compatibility\nand Robust Dense-Phase Relaxation"],"prefix":"10.1021","volume":"66","author":[{"given":"Xiaojing","family":"Tian","sequence":"first","affiliation":[{"name":"Peking University Shenzhen Graduate School , , ,","place":["Shenzhen, China, 518055"]},{"name":"Shenzhen Bay Laboratory , , ,","place":["Shenzhen, China, 518132"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0759-1766","authenticated-orcid":true,"given":"Wei","family":"Han","sequence":"additional","affiliation":[{"name":"Hong Kong Baptist University , , , ,","place":["Hong Kong, SAR, China, 999077"]},{"name":"Hong Kong Baptist University , , ,","place":["Shenzhen, China, 518000"]},{"name":"Shenzhen Bay Laboratory , , ,","place":["Shenzhen, China, 518132"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,6,30]]},"reference":[{"issue":"7","key":"2026090711203386400_cit1","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.1016\/j.cell.2016.04.047","article-title":"Coexisting\nLiquid Phases Underlie Nucleolar Subcompartments","volume":"165","author":"Feric","year":"2016","journal-title":"Cell"},{"issue":"1","key":"2026090711203386400_cit2","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.cell.2015.09.015","article-title":"Phase Separation\nby Low Complexity Domains Promotes Stress Granule Assembly and Drives\nPathological Fibrillization","volume":"163","author":"Molliex","year":"2015","journal-title":"Cell"},{"issue":"6","key":"2026090711203386400_cit3","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1038\/s41589-021-00801-x","article-title":"Mechanistic Dissection of Increased Enzymatic Rate\nin a Phase-Separated Compartment","volume":"17","author":"Peeples","year":"2021","journal-title":"Nat. Chem.\nBiol."},{"issue":"3","key":"2026090711203386400_cit4","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.cell.2018.12.035","article-title":"Considerations and\nChallenges in\nStudying Liquid-Liquid Phase Separation and Biomolecular Condensates","volume":"176","author":"Alberti","year":"2019","journal-title":"Cell"},{"key":"2026090711203386400_cit5","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1146\/annurev-physchem-082423-032133","article-title":"Computational Modeling of Biomolecular\nPhase Separation:\nCurrent Progress and Open Challenges","volume":"77","author":"Rizuan","year":"2026","journal-title":"Annu.\nRev. Phys. Chem."},{"issue":"1","key":"2026090711203386400_cit6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005941","article-title":"Sequence Determinants\nof Protein Phase Behavior from a Coarse-Grained Model","volume":"14","author":"Dignon","year":"2018","journal-title":"PLOS Comput. 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Theory Comput."},{"issue":"1","key":"2026090711203386400_cit29","doi-asserted-by":"publisher","first-page":"10562","DOI":"10.1038\/s41467-025-65603-4","article-title":"Optimized Protein-Water Interactions\nand Torsional Refinements Yield Balanced Atomistic Protein Force Fields","volume":"16","author":"Phan","year":"2025","journal-title":"Nat. Commun."},{"key":"2026090711203386400_cit30","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High Performance\nMolecular Simulations through Multi-Level Parallelism from Laptops\nto Supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"issue":"1","key":"2026090711203386400_cit31","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1021\/acs.jpcb.3c06662","article-title":"OpenMM 8: Molecular Dynamics Simulation with Machine\nLearning Potentials","volume":"128","author":"Eastman","year":"2024","journal-title":"J. Phys. Chem. 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Eur."},{"issue":"11","key":"2026090711203386400_cit34","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5172","article-title":"A Coarse-Grained\nModel for Disordered and Multi-Domain Proteins","volume":"33","author":"Cao","year":"2024","journal-title":"Protein Sci."},{"issue":"7","key":"2026090711203386400_cit35","doi-asserted-by":"publisher","first-page":"1371","DOI":"10.1002\/pro.4094","article-title":"Improved Coarse-grained\nModel for Studying Sequence Dependent Phase Separation of Disordered\nProteins","volume":"30","author":"Regy","year":"2021","journal-title":"Protein Sci."},{"issue":"4","key":"2026090711203386400_cit36","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1021\/acs.jctc.4c01460","article-title":"COCOMO2: A Coarse-Grained\nModel for Interacting Folded and Disordered Proteins","volume":"21","author":"Jussupow","year":"2025","journal-title":"J. Chem. Theory Comput."},{"issue":"2","key":"2026090711203386400_cit37","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1021\/acscentsci.4c01617","article-title":"Chemically\nInformed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular\nCondensates","volume":"11","author":"Tejedor","year":"2025","journal-title":"ACS Cent. Sci."},{"issue":"3","key":"2026090711203386400_cit38","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.cpc.2005.01.020","article-title":"Shortest Multiple\nDisconnected Path for the Analysis of Entanglements in Two- and Three-Dimensional\nPolymeric Systems","volume":"168","author":"Kro\u0308ger","year":"2005","journal-title":"Comput. Phys. 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Bioinforma."},{"issue":"44","key":"2026090711203386400_cit42","doi-asserted-by":"publisher","first-page":"17874","DOI":"10.1073\/pnas.1311599110","article-title":"Native\nContacts Determine Protein\nFolding Mechanisms in Atomistic Simulations","volume":"110","author":"Best","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"8","key":"2026090711203386400_cit43","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1038\/s41592-019-0506-8","article-title":"The PLUMED consortium. Promoting\nTransparency and Reproducibility in Enhanced Molecular Simulations","volume":"16","author":"Bonomi","year":"2019","journal-title":"Nat. Methods"},{"issue":"3","key":"2026090711203386400_cit44","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.cell.2018.06.006","article-title":"A Molecular Grammar\nGoverning the Driving Forces for\nPhase Separation of Prion-like RNA Binding Proteins","volume":"174","author":"Wang","year":"2018","journal-title":"Cell"},{"issue":"7","key":"2026090711203386400_cit45","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/s41594-019-0250-x","article-title":"Molecular Interactions Underlying\nLiquid\u2013liquid Phase Separation of the FUS Low-Complexity Domain","volume":"26","author":"Murthy","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"issue":"23","key":"2026090711203386400_cit46","doi-asserted-by":"publisher","DOI":"10.1063\/1.2121687","article-title":"A General Purpose Model\nfor the Condensed Phases of\nWater: TIP4P\/2005","volume":"123","author":"Abascal","year":"2005","journal-title":"J. Chem. 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Biol."},{"key":"2026090711203386400_cit50","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2025.103120","article-title":"Probing Molecular\nand Biophysical Mechanisms of RNA\nand Protein Phase Transitions with Simulations and Theory","volume":"93","author":"Chew","year":"2025","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026090711203386400_cit51","doi-asserted-by":"publisher","first-page":"5895","DOI":"10.1101\/2025.06.26.661889","article-title":"StruCloze: A Unified Framework\nfor\nBackmapping and Inpainting of Biomolecules","volume":"22","author":"Zhu","year":"2026","journal-title":"J. Chem. Theory Comput."},{"key":"2026090711203386400_cit52","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2022.108567","article-title":"The Z1+ Package: Shortest\nMultiple Disconnected Path for the Analysis of Entanglements in Macromolecular\nSystems","volume":"283","author":"Kro\u0308ger","year":"2023","journal-title":"Comput. Phys. Commun."},{"issue":"37","key":"2026090711203386400_cit53","doi-asserted-by":"publisher","first-page":"33723","DOI":"10.1021\/jacs.5c09558","article-title":"Molecular Simulations with a Pretrained\nNeural Network\nand Universal Pairwise Force Fields","volume":"147","author":"Kabylda","year":"2025","journal-title":"J. Am.\nChem. Soc."},{"issue":"21","key":"2026090711203386400_cit54","doi-asserted-by":"publisher","first-page":"17598","DOI":"10.1021\/jacs.4c07099","article-title":"MACE-OFF: Short-Range Transferable\nMachine Learning Force Fields for Organic Molecules","volume":"147","author":"Kova\u0301cs","year":"2025","journal-title":"J. Am. Chem. Soc."}],"container-title":["Journal of Chemical Information\nand Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c00413","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/13\/7337\/65289026\/acs.jcim.6c00413.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/13\/7337\/65289026\/acs.jcim.6c00413.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T15:24:21Z","timestamp":1788794661000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/13\/7337\/5171238\/CondenSimAdapter-A-Versatile-Builder-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,30]]},"references-count":54,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2026,6,30]]},"published-print":{"date-parts":[[2026,7,13]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c00413","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,30]]}}}