{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T23:10:37Z","timestamp":1777504237534,"version":"3.51.4"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,11,10]],"date-time":"2017-11-10T00:00:00Z","timestamp":1510272000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2017,11,10]],"date-time":"2017-11-10T00:00:00Z","timestamp":1510272000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000076","name":"Directorate for Biological Sciences","doi-asserted-by":"publisher","award":["DBI-0953839"],"award-info":[{"award-number":["DBI-0953839"]}],"id":[{"id":"10.13039\/100000076","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM109980"],"award-info":[{"award-number":["R01GM109980"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000968","name":"American Heart Association","doi-asserted-by":"publisher","award":["13GRNT16990076"],"award-info":[{"award-number":["13GRNT16990076"]}],"id":[{"id":"10.13039\/100000968","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000083","name":"Directorate for Computer and Information Science and Engineering","doi-asserted-by":"publisher","award":["CNS-1429294"],"award-info":[{"award-number":["CNS-1429294"]}],"id":[{"id":"10.13039\/100000083","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2018,1]]},"DOI":"10.1007\/s10822-017-0082-x","type":"journal-article","created":{"date-parts":[[2017,11,10]],"date-time":"2017-11-10T05:53:32Z","timestamp":1510293212000},"page":"103-111","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor"],"prefix":"10.1007","volume":"32","author":[{"given":"Rui","family":"Duan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianjin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0637-8648","authenticated-orcid":false,"given":"Xiaoqin","family":"Zou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,11,10]]},"reference":[{"key":"82_CR1","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1007\/s10822-016-9946-8","volume":"30","author":"S Gathiaka","year":"2016","unstructured":"Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK (2016) D3R Grand Challenge 2015: evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des 30:651\u2013668","journal-title":"J Comput Aided Mol Des"},{"key":"82_CR2","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1016\/0092-8674(95)90530-8","volume":"81","author":"BM Forman","year":"1995","unstructured":"Forman BM, Ode E, Chen J, Oro AE, Bradley DJ, Perlmann T, Noonan DJ, Burka LT, McMorris T, Lamph WW, Evans RM, Weinberger C (1995) Identification of a nuclear receptor that is activated by farnesol metabolites. Cell 81:687\u2013693","journal-title":"Cell"},{"key":"82_CR3","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1126\/science.284.5418.1365","volume":"284","author":"DJ Parks","year":"1999","unstructured":"Parks DJ, Blanchard SG, Bledsoe RK, Chandra G, Consler TG, Kliewer SA, Stimmel JB, Willson TM, Zavacki AM, Moore DD, Lehmann JM (1999) Bile acids: natural ligands for an orphan nuclear receptor. Science 284:1365\u20131368","journal-title":"Science"},{"key":"82_CR4","doi-asserted-by":"publisher","first-page":"2563","DOI":"10.1074\/jbc.M209525200","volume":"278","author":"G Lambert","year":"2003","unstructured":"Lambert G, Amar MJ, Guo G, Brewer HB Jr, Gonzalez FJ, Sinal CJ (2003) The farnesoid X-receptor is an essential regulator of cholesterol homeostasis. J Biol Chem 278:2563\u20132570","journal-title":"J Biol Chem"},{"key":"82_CR5","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1172\/JCI25604","volume":"116","author":"K Ma","year":"2006","unstructured":"Ma K, Saha PK, Chan L, Moore DD (2006) Farnesoid X receptor is essential for normal glucose homeostasis. J Clin Invest 116:1102\u20131109","journal-title":"J Clin Invest"},{"key":"82_CR6","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1016\/S0092-8674(00)00062-3","volume":"102","author":"CJ Sinal","year":"2000","unstructured":"Sinal CJ, Tohkin M, Miyata M, Ward JM, Lambert G, Gonzalez FJ (2000) Targeted disruption of the nuclear receptor FXR\/BAR impairs bile acid and lipid homeostasis. Cell 102:731\u2013744","journal-title":"Cell"},{"key":"82_CR7","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1210\/me.2011-1157","volume":"26","author":"Y Zhang","year":"2012","unstructured":"Zhang Y, Ge X, Heemstra LA, Chen WD, Xu J, Smith JL, Ma H, Kasim N, Edwards PA, Novak CM (2012) Loss of FXR protects against diet-induced obesity and accelerates liver carcinogenesis in ob\/ob mice. Mol Endocrinol 26:272\u2013280","journal-title":"Mol Endocrinol"},{"key":"82_CR8","doi-asserted-by":"publisher","first-page":"11039","DOI":"10.1074\/jbc.M510258200","volume":"281","author":"B Cariou","year":"2006","unstructured":"Cariou B, van Harmelen K, Duran-Sandoval D, van Dijk TH, Grefhorst A, Abdelkarim M, Caron S, Torpier G, Fruchart J, Gonzalez FJ, Kuipers F, Staels B (2006) The farnesoid X receptor modulates adiposity and peripheral insulin sensitivity in mice. J Biol Chem 281:11039\u201311049","journal-title":"J Biol Chem"},{"key":"82_CR9","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1007\/s10822-017-0038-1","volume":"31","author":"X Xu","year":"2017","unstructured":"Xu X, Yan C, Zou X (2017) Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R GRAND challenge 2015. J Comput Aided Mol Des 31:689\u2013699","journal-title":"J Comput Aided Mol Des"},{"key":"82_CR10","doi-asserted-by":"publisher","first-page":"2372","DOI":"10.1021\/ci200060s","volume":"51","author":"X Liu","year":"2011","unstructured":"Liu X, Jiang H, Li H (2011) SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening. J Chem Inf Model 51:2372\u20132385","journal-title":"J Chem Inf Model"},{"key":"82_CR11","doi-asserted-by":"publisher","first-page":"3564","DOI":"10.1021\/jm200139j","volume":"54","author":"W Lu","year":"2011","unstructured":"Lu W, Liu X, Cao X, Xue M, Liu K, Zhao Z, Shen X, Jiang H, Xu Y, Huang J, Li H (2011) SHAFTS: a hybrid approach for 3D molecular similarity calculation. 2. Prospective case study in the discovery of diverse P90 ribosomal S6 protein kinase 2 inhibitors to suppress cell migration. J Med Chem 54:3564\u20133574","journal-title":"J Med Chem"},{"key":"82_CR12","first-page":"983","volume":"38","author":"P Willett","year":"1998","unstructured":"Willett P, Barnard JM, Downs GM (1998) Chemical similarity searching. J Chem Inf Model 38:983\u2013996","journal-title":"J Chem Inf Model"},{"key":"82_CR13","doi-asserted-by":"publisher","first-page":"3204","DOI":"10.1039\/b409813g","volume":"2","author":"A Bender","year":"2004","unstructured":"Bender A, Glen RC (2004) Molecular similarity: a key technique in molecular informatics. Org Biomol Chem 2:3204\u20133218","journal-title":"Org Biomol Chem"},{"key":"82_CR14","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1021\/ci9000053","volume":"49","author":"T Cheng","year":"2009","unstructured":"Cheng T, Li X, Li Y, Liu Z, Wang R (2009) Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 49:1079\u20131093","journal-title":"J Chem Inf Model"},{"key":"82_CR15","doi-asserted-by":"publisher","first-page":"4111","DOI":"10.1021\/jm048957q","volume":"48","author":"R Wang","year":"2005","unstructured":"Wang R, Fang X, Lu Y, Yang CY, Wang S (2005) The PDBbind database: methodologies and updates. J Med Chem 48:4111\u20134119","journal-title":"J Med Chem"},{"key":"82_CR16","doi-asserted-by":"publisher","first-page":"1866","DOI":"10.1002\/jcc.20504","volume":"27","author":"S Huang","year":"2006","unstructured":"Huang S, Zou X (2006) An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 27:1866\u20131875","journal-title":"J Comput Chem"},{"key":"82_CR17","doi-asserted-by":"publisher","first-page":"1876","DOI":"10.1002\/jcc.20505","volume":"27","author":"S Huang","year":"2006","unstructured":"Huang S, Zou X (2006) An iterative knowledge-based scoring function to predict protein\u2013ligand interactions: II. Validation of the scoring function. J Comput Chem 27:1876\u20131882","journal-title":"J Comput Chem"},{"key":"82_CR18","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1021\/acs.jcim.5b00504","volume":"56","author":"C Yan","year":"2016","unstructured":"Yan C, Grinter SZ, Merideth BR, Ma Z, Zou X (2016) Iterative knowledge-based scoring functions derived from rigid and flexible decoy structures: evaluation with the 2013 and 2014 CSAR benchmarks. J Chem Inf Model 56:1013\u20131021","journal-title":"J Chem Inf Model"},{"key":"82_CR19","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1021\/ar000033j","volume":"33","author":"PA Kollman","year":"2000","unstructured":"Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889\u2013897","journal-title":"Acc Chem Res"},{"key":"82_CR20","doi-asserted-by":"publisher","first-page":"9401","DOI":"10.1021\/ja981844+","volume":"120","author":"J Srinivasan","year":"1998","unstructured":"Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate\u2013DNA helices. J Am Chem Soc 120:9401\u20139409","journal-title":"J Am Chem Soc"},{"key":"82_CR21","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1021\/ci100031x","volume":"50","author":"PC Hawkins","year":"2010","unstructured":"Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer generation with omega: algorithm and validation using high quality structures from the protein databank and cambridge structural database. J Chem Inf Model 50:572\u2013584","journal-title":"J Chem Inf Model"},{"key":"82_CR22","doi-asserted-by":"publisher","first-page":"2919","DOI":"10.1021\/ci300314k","volume":"52","author":"PC Hawkins","year":"2012","unstructured":"Hawkins PC, Nicholls A (2012) Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model 52:2919\u20132936","journal-title":"J Chem Inf Model"},{"key":"82_CR23","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455\u2013461","journal-title":"J Comput Chem"},{"key":"82_CR24","volume-title":"AMBER 11","author":"DA Case","year":"2010","unstructured":"Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossv\u00e1ry I, Wong KF, Paesani F, Vanicek J, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2010) AMBER 11. University of California, San Francisco"},{"key":"82_CR25","doi-asserted-by":"publisher","first-page":"3902","DOI":"10.1021\/ja00299a024","volume":"107","author":"MJS Dewar","year":"1985","unstructured":"Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107:3902\u20133909","journal-title":"J Am Chem Soc"},{"key":"82_CR26","volume-title":"Gaussian 09, revision D.01","author":"MJ Frisch","year":"2009","unstructured":"Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas \u00d6, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, revision D.01. Gaussian, Inc., Wallingford"},{"key":"82_CR27","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1002\/jcc.10128","volume":"23","author":"A Jakalian","year":"2002","unstructured":"Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23:1623\u20131641","journal-title":"J Comput Chem"},{"key":"82_CR28","doi-asserted-by":"publisher","first-page":"1999","DOI":"10.1002\/jcc.10349","volume":"24","author":"Y Duan","year":"2003","unstructured":"Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999\u20132012","journal-title":"J Comput Chem"},{"key":"82_CR29","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"J Wang","year":"2004","unstructured":"Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157\u20131174","journal-title":"J Comput Chem"},{"key":"82_CR30","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) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926\u2013935","journal-title":"J Chem Phys"},{"key":"82_CR31","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N\u22c5log(N) method for Ewald sums in large systems. J Chem Phys 98:10089\u201310092","journal-title":"J Chem Phys"},{"key":"82_CR32","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1080\/00268978800101881","volume":"65","author":"RW Pastor","year":"1988","unstructured":"Pastor RW, Brooks BR, Szabo A (1988) An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys 65:1409\u20131419","journal-title":"Mol Phys"},{"key":"82_CR33","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"JP Ryckaert","year":"1977","unstructured":"Ryckaert JP, Ciccotti G, Berendsen HJ (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327\u2013341","journal-title":"J Comput Phys"},{"key":"82_CR34","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1002\/jcc.10120","volume":"23","author":"R Luo","year":"2002","unstructured":"Luo R, David L, Gilson MK (2002) Accelerated Poisson\u2013Boltzmann calculations for static and dynamic systems. J Comput Chem 23:1244\u20131253","journal-title":"J Comput Chem"},{"key":"82_CR35","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.1021\/j100058a043","volume":"98","author":"D Sitkoff","year":"1994","unstructured":"Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978\u20131988","journal-title":"J Phys Chem"},{"key":"82_CR36","doi-asserted-by":"publisher","first-page":"4020","DOI":"10.1021\/j100265a018","volume":"89","author":"DT Nguyen","year":"1985","unstructured":"Nguyen DT, Case DA (1985) On finding stationary states of large molecule potential energy surfaces. J Phys Chem 89:4020\u20134026","journal-title":"J Phys Chem"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-017-0082-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0082-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0082-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T14:15:23Z","timestamp":1719584123000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-017-0082-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,10]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1]]}},"alternative-id":["82"],"URL":"https:\/\/doi.org\/10.1007\/s10822-017-0082-x","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,10]]},"assertion":[{"value":"15 June 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 November 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 November 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}