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These distances are then used in multidimensional scaling to produce 3D geometries, subsequently refined with standard bioorganic forcefields. The machine learning\u2010based graph distance introduced herein is found to be an improvement over the conventional shortest path distances used in graph drawing. Comparative analysis with a state\u2010of\u2010the\u2010art distance geometry method demonstrates nGDE's competitive performance, particularly showcasing robustness in handling polycyclic molecules\u2014a challenge for existing methods.<\/jats:p>","DOI":"10.1002\/jcc.27349","type":"journal-article","created":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T10:39:56Z","timestamp":1713955196000},"page":"1784-1790","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Neural graph distance embedding for molecular geometry generation"],"prefix":"10.1002","volume":"45","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-0862-5289","authenticated-orcid":false,"given":"Johannes T.","family":"Margraf","sequence":"first","affiliation":[{"name":"Bavarian Center for Battery Technology (BayBatt) University of Bayreuth Bayreuth Germany"}]}],"member":"311","published-online":{"date-parts":[[2024,4,24]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci2004658"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00221"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.9b00576"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00915"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-020-00236-4"},{"key":"e_1_2_8_7_1","first-page":"11423","volume-title":"Advances in Neural Information Processing Systems","author":"Batatia I.","year":"2022"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29939-5"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1088\/2632-2153\/ac9955"},{"key":"e_1_2_8_10_1","volume-title":"Advances in Neural Information Processing Systems","author":"Gasteiger J.","year":"2021"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1093-3263(97)00014-4"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5b00654"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00025"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24525-7"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/0925-7721(94)00014-X"},{"key":"e_1_2_8_17_1","unstructured":"S. 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