{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T17:38:15Z","timestamp":1772127495774,"version":"3.50.1"},"reference-count":57,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T00:00:00Z","timestamp":1745884800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T00:00:00Z","timestamp":1745884800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T00:00:00Z","timestamp":1745884800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000121","name":"Division of Mathematical Sciences","doi-asserted-by":"publisher","award":["DMS-1563234"],"award-info":[{"award-number":["DMS-1563234"]}],"id":[{"id":"10.13039\/100000121","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000121","name":"Division of Mathematical Sciences","doi-asserted-by":"publisher","award":["DMS-1564480"],"award-info":[{"award-number":["DMS-1564480"]}],"id":[{"id":"10.13039\/100000121","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001502","name":"Department of Atomic Energy, Government of India","doi-asserted-by":"publisher","award":["RTI 4006"],"award-info":[{"award-number":["RTI 4006"]}],"id":[{"id":"10.13039\/501100001502","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["SPG\/2020\/000475"],"award-info":[{"award-number":["SPG\/2020\/000475"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR40323\/BTIS\/137\/78\/2023"],"award-info":[{"award-number":["BT\/PR40323\/BTIS\/137\/78\/2023"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2025,5,12]]},"DOI":"10.1021\/acs.jcim.4c02412","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T14:08:07Z","timestamp":1745935687000},"page":"4576-4592","source":"Crossref","is-referenced-by-count":1,"title":["A New Discrete-Geometry Approach for Integrative Docking of Proteins Using Chemical Cross-Links"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7131-7262","authenticated-orcid":true,"given":"Yichi","family":"Zhang","sequence":"first","affiliation":[{"name":"CISE Department","place":["Gainesville, United States"]},{"name":"University of Florida","place":["Gainesville, United States"]}]},{"given":"Muskaan","family":"Jindal","sequence":"additional","affiliation":[{"name":"National Center for Biological Sciences","place":["Bengaluru, India"]},{"name":"Tata Institute of Fundamental Research","place":["Bengaluru, India"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9061-8407","authenticated-orcid":true,"given":"Shruthi","family":"Viswanath","sequence":"additional","affiliation":[{"name":"National Center for Biological Sciences","place":["Bengaluru, India"]},{"name":"Tata Institute of Fundamental Research","place":["Bengaluru, India"]}]},{"given":"Meera","family":"Sitharam","sequence":"additional","affiliation":[{"name":"CISE Department","place":["Gainesville, United States"]},{"name":"University of Florida","place":["Gainesville, United States"]}]}],"member":"316","published-online":{"date-parts":[[2025,4,29]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.26609"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-102622-084607"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-013118-111429"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2019.11.009"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.05.016"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001244"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9608-7_15"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts628"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2010.10.014"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2023.102357"},{"key":"ref11\/cit11","unstructured":"Arvindekar, S.; Majila, K.; Viswanath, S. Recent methods from statistical inference and machine learning to improve integrative modeling of macromolecular assemblies. 2024, arXiv:2401.17894. arXiv preprint."},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.12.017"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2021.11.007"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/ja026939x"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-024-01011-0"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-021-00640-z"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3995"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3838"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2021.100139"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01704-z"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51771-2"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1063\/5.0141474"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4387"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.3390\/life11111183"},{"key":"ref25\/cit25","unstructured":"Ozkan, A.; Sitharam, M. EASAL (Efficient Atlasing, Analysis and Search of Molecular Assembly Landscapes). In\n                      Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology\n                      ; ISCA, 2011; pp 233\u2013238."},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00763"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00945"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1145\/3204472"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1008357"},{"key":"ref30\/cit30","unstructured":"Zhang, Y.; Sitharam, M. Best of two worlds: Cartesian sampling and volume computation for high dimensional configuration spaces using Cayley coordinates. In\n                      Proceedings of the 30th Fall Workshop on Computational Geometry, NCSU\n                      , 2022."},{"key":"ref31\/cit31","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Sitharam, M. Best of two worlds: Cartesian sampling and volume computation for distance-constrained configuration spaces using Cayley coordinates. 2024. arXiv:2408.16946. http:\/\/arxiv.org\/abs\/2408.16946 (accessed April 28, 2025).","DOI":"10.1007\/s00500-023-08441-0"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33729-4"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae329"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02174-0"},{"key":"ref35\/cit35","volume-title":"Handbook of Geometric Constraint Systems Principles","author":"Sitharam M.","year":"2019"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1007\/s00454-009-9160-8"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-21362-0_9"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2021.01.005"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.15252\/msb.202311544"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M116.058560"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2018.04.016"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M114.041673"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2020.07.010"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1002\/pro.2458"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2318601121"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5217"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2017.10.005"},{"key":"ref48\/cit48","unstructured":"Ozkan, A.; Sitharam, M. Best of Both Worlds: Uniform sampling in Cartesian and Cayley Molecular Assembly Configuration Space. 2014. arXiv:1409.0956. http:\/\/arxiv.org\/abs\/1409.0956 (accessed April 28, 2025)."},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2014.08.001"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1111\/febs.16435"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2219418120"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-04773-7"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2609-2_14"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1016\/bs.mie.2022.11.003"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1101\/2023.11.17.567543"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202200341"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c02412","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c02412","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T04:11:14Z","timestamp":1747023074000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c02412"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,29]]},"references-count":57,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,5,12]]}},"alternative-id":["10.1021\/acs.jcim.4c02412"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.4c02412","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.10.24.619977","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,29]]}}}