{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T01:34:50Z","timestamp":1777080890500,"version":"3.51.4"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T00:00:00Z","timestamp":1777075200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T00:00:00Z","timestamp":1777075200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"DOI":"10.1007\/s10822-026-00811-8","type":"journal-article","created":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T01:02:29Z","timestamp":1777078949000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Quantifying conformational diversity in protein\u2013ligand ensembles for structure-based virtual screening"],"prefix":"10.1007","volume":"40","author":[{"given":"Pei\u2212Kun","family":"Yang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,4,25]]},"reference":[{"issue":"2","key":"811_CR1","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) J Comput Chem 31(2):455","journal-title":"J Comput Chem"},{"issue":"1","key":"811_CR2","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s13321-021-00522-2","volume":"13","author":"AT McNutt","year":"2021","unstructured":"McNutt AT, Francoeur P, Aggarwal R, Masuda T, Meli R, Ragoza M, Sunseri J, Koes DR (2021) J Cheminform 13(1):43","journal-title":"J Cheminform"},{"issue":"2","key":"811_CR3","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s12551-016-0247-1","volume":"9","author":"NS Pagadala","year":"2017","unstructured":"Pagadala NS, Syed K, Tuszynski J (2017) Biophys Rev 9(2):91","journal-title":"Biophys Rev"},{"issue":"9","key":"811_CR4","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1021\/cn3000422","volume":"3","author":"JL Reymond","year":"2012","unstructured":"Reymond JL, Awale M (2012) ACS Chem Neurosci 3(9):649","journal-title":"ACS Chem Neurosci"},{"issue":"4","key":"811_CR5","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1021\/acs.jcim.2c01253","volume":"63","author":"BI Tingle","year":"2023","unstructured":"Tingle BI, Tang KG, Castanon M, Gutierrez JJ, Khurelbaatar M, Dandarchuluun C, Moroz YS, Irwin JJ (2023) J Chem Inf Model 63(4):1166","journal-title":"J Chem Inf Model"},{"issue":"1","key":"811_CR6","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1002\/pro.3934","volume":"30","author":"DS Goodsell","year":"2021","unstructured":"Goodsell DS, Sanner MF, Olson AJ, Forli S (2021) Protein Sci 30(1):31","journal-title":"Protein Sci"},{"key":"811_CR7","doi-asserted-by":"publisher","first-page":"343","DOI":"10.3389\/fchem.2020.00343","volume":"8","author":"EHB Maia","year":"2020","unstructured":"Maia EHB, Assis LC, de Oliveira TA, da Silva AM, Taranto AG (2020) Front Chem 8:343","journal-title":"Front Chem"},{"issue":"9","key":"811_CR8","doi-asserted-by":"publisher","first-page":"3906","DOI":"10.3390\/molecules28093906","volume":"28","author":"D Bassani","year":"2023","unstructured":"Bassani D, Moro S (2023) Molecules 28(9):3906","journal-title":"Molecules"},{"issue":"1","key":"811_CR9","doi-asserted-by":"publisher","first-page":"22","DOI":"10.3390\/ph17010022","volume":"17","author":"SK Niazi","year":"2023","unstructured":"Niazi SK, Mariam Z (2023) Pharmaceuticals (Basel) 17(1):22","journal-title":"Pharmaceuticals (Basel)"},{"issue":"D1","key":"811_CR10","first-page":"D271","volume":"45","author":"PW Rose","year":"2017","unstructured":"Rose PW, Prlic A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK (2017) Nucleic Acids Res 45(D1):D271","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"811_CR11","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/nrd1129","volume":"2","author":"SJ Teague","year":"2003","unstructured":"Teague SJ (2003) Nat Rev Drug Discov 2(7):527","journal-title":"Nat Rev Drug Discov"},{"issue":"11","key":"811_CR12","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/nchembio.232","volume":"5","author":"DD Boehr","year":"2009","unstructured":"Boehr DD, Nussinov R, Wright PE (2009) Nat Chem Biol 5(11):789","journal-title":"Nat Chem Biol"},{"issue":"4","key":"811_CR13","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1023\/A:1008007507641","volume":"12","author":"J Bostrom","year":"1998","unstructured":"Bostrom J, Norrby PO, Liljefors T (1998) J Comput Aided Mol Des 12(4):383","journal-title":"J Comput Aided Mol Des"},{"issue":"10","key":"811_CR14","doi-asserted-by":"publisher","first-page":"2499","DOI":"10.1021\/jm030563w","volume":"47","author":"E Perola","year":"2004","unstructured":"Perola E, Charifson PS (2004) J Med Chem 47(10):2499","journal-title":"J Med Chem"},{"issue":"7","key":"811_CR15","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.1021\/ja512751q","volume":"137","author":"L Wang","year":"2015","unstructured":"Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R (2015) J Am Chem Soc 137(7):2695","journal-title":"J Am Chem Soc"},{"key":"811_CR16","doi-asserted-by":"crossref","unstructured":"Fu H, Chen H, Blazhynska M, Goulard Coderc de Lacam E, Szczepaniak F, Pavlova A, Shao X, Gumbart JC, Dehez F, Roux B, Cai W, Chipot C (2022) Nat Protoc 17(4):1114","DOI":"10.1038\/s41596-021-00676-1"},{"issue":"1","key":"811_CR17","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1186\/s12859-014-0399-6","volume":"15","author":"L Skjaerven","year":"2014","unstructured":"Skjaerven L, Yao XQ, Scarabelli G, Grant BJ (2014) BMC Bioinform 15(1):399","journal-title":"BMC Bioinform"},{"issue":"S10","key":"811_CR18","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1002\/qua.560240721","volume":"24","author":"M Levitt","year":"1983","unstructured":"Levitt M, Sander C, Stern PS (1983) Int J Quantum Chem 24(S10):181","journal-title":"Int J Quantum Chem"},{"issue":"20","key":"811_CR19","doi-asserted-by":"publisher","first-page":"12562","DOI":"10.1073\/pnas.202427399","volume":"99","author":"A Laio","year":"2002","unstructured":"Laio A, Parrinello M (2002) Proc Natl Acad Sci USA 99(20):12562","journal-title":"Proc Natl Acad Sci USA"},{"issue":"24","key":"811_CR20","doi-asserted-by":"publisher","first-page":"11919","DOI":"10.1063\/1.1755656","volume":"120","author":"D Hamelberg","year":"2004","unstructured":"Hamelberg D, Mongan J, McCammon JA (2004) J Chem Phys 120(24):11919","journal-title":"J Chem Phys"},{"issue":"9","key":"811_CR21","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/nsb0902-646","volume":"9","author":"M Karplus","year":"2002","unstructured":"Karplus M, McCammon JA (2002) Nat Struct Biol 9(9):646","journal-title":"Nat Struct Biol"},{"key":"811_CR22","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-biophys-042910-155245","volume":"41","author":"RO Dror","year":"2012","unstructured":"Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE (2012) Annu Rev Biophys 41:429","journal-title":"Annu Rev Biophys"},{"issue":"15","key":"811_CR23","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1002\/jcc.24660","volume":"38","author":"S Jo","year":"2017","unstructured":"Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD Jr, Klauda JB, Qi Y, Im W (2017) J Comput Chem 38(15):1114","journal-title":"J Comput Chem"},{"issue":"9","key":"811_CR24","doi-asserted-by":"publisher","first-page":"3257","DOI":"10.1021\/ct300400x","volume":"8","author":"RB Best","year":"2012","unstructured":"Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, MacKerell AD Jr (2012) J Chem Theory Comput 8(9):3257","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"811_CR25","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.4067","volume":"14","author":"J Huang","year":"2017","unstructured":"Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmuller H, MacKerell AD Jr (2017) Nat Methods 14(1):71","journal-title":"Nat Methods"},{"issue":"4","key":"811_CR26","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"K Vanommeslaeghe","year":"2010","unstructured":"Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2010) J Comput Chem 31(4):671","journal-title":"J Comput Chem"},{"issue":"12","key":"811_CR27","doi-asserted-by":"publisher","first-page":"3144","DOI":"10.1021\/ci300363c","volume":"52","author":"K Vanommeslaeghe","year":"2012","unstructured":"Vanommeslaeghe K, MacKerell AD Jr (2012) J Chem Inf Model 52(12):3144","journal-title":"J Chem Inf Model"},{"issue":"12","key":"811_CR28","doi-asserted-by":"publisher","first-page":"3155","DOI":"10.1021\/ci3003649","volume":"52","author":"K Vanommeslaeghe","year":"2012","unstructured":"Vanommeslaeghe K, Raman EP, MacKerell AD Jr (2012) J Chem Inf Model 52(12):3155","journal-title":"J Chem Inf Model"},{"issue":"2","key":"811_CR29","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79(2):926","journal-title":"J Chem Phys"},{"issue":"8","key":"811_CR30","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1021\/j100059a038","volume":"98","author":"SR Durell","year":"1994","unstructured":"Durell SR, Brooks BR, Ben-Naim A (1994) J Phys Chem 98(8):2198","journal-title":"J Phys Chem"},{"issue":"1","key":"811_CR31","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1021\/acs.jpcb.3c06662","volume":"128","author":"P Eastman","year":"2023","unstructured":"Eastman P, Galvelis R, Pel\u00e1ez RP, Abreu CR, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J (2023) J Phys Chem B 128(1):109","journal-title":"J Phys Chem B"},{"issue":"3","key":"811_CR32","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"J-P Ryckaert","year":"1977","unstructured":"Ryckaert J-P, Ciccotti G, Berendsen HJ (1977) J Comput Phys 23(3):327","journal-title":"J Comput Phys"},{"issue":"8","key":"811_CR33","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","volume":"109","author":"RT McGibbon","year":"2015","unstructured":"McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernandez CX, Schwantes CR, Wang LP, Lane TJ, Pande VS (2015) Biophys J 109(8):1528","journal-title":"Biophys J"},{"issue":"8016","key":"811_CR34","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","volume":"630","author":"J Abramson","year":"2024","unstructured":"Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J (2024) Nature 630(8016):493","journal-title":"Nature"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-026-00811-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-026-00811-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-026-00811-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T01:02:30Z","timestamp":1777078950000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-026-00811-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,25]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["811"],"URL":"https:\/\/doi.org\/10.1007\/s10822-026-00811-8","relation":{},"ISSN":["1573-4951"],"issn-type":[{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,25]]},"assertion":[{"value":"23 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"104"}}