{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T07:35:03Z","timestamp":1765438503540,"version":"3.37.3"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,8,24]],"date-time":"2017-08-24T00:00:00Z","timestamp":1503532800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"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\/s10822-017-0051-4","type":"journal-article","created":{"date-parts":[[2017,8,24]],"date-time":"2017-08-24T04:10:34Z","timestamp":1503547834000},"page":"251-264","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2"],"prefix":"10.1007","volume":"32","author":[{"given":"Veronica","family":"Salmaso","sequence":"first","affiliation":[]},{"given":"Mattia","family":"Sturlese","sequence":"additional","affiliation":[]},{"given":"Alberto","family":"Cuzzolin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7514-3802","authenticated-orcid":false,"given":"Stefano","family":"Moro","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,8,24]]},"reference":[{"key":"51_CR1","doi-asserted-by":"crossref","first-page":"127","DOI":"10.2174\/156802610790232251","volume":"10","author":"TT Talele","year":"2010","unstructured":"Talele TT, Khedkar SA, Rigby AC (2010) Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. Curr Top Med Chem 10:127\u2013141","journal-title":"Curr Top Med Chem"},{"key":"51_CR2","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/0022-2836(82)90153-X","volume":"161","author":"ID Kuntz","year":"1982","unstructured":"Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to macromolecule\u2013ligand interactions. J Mol Biol 161:269\u2013288","journal-title":"J Mol Biol"},{"key":"51_CR3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235\u2013242","journal-title":"Nucleic Acids Res"},{"key":"51_CR4","doi-asserted-by":"crossref","first-page":"2895","DOI":"10.1021\/jm0300330","volume":"46","author":"SL McGovern","year":"2003","unstructured":"McGovern SL, Shoichet BK (2003) Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 46:2895\u20132907","journal-title":"J Med Chem"},{"key":"51_CR5","unstructured":"Directory of in silico Drug Design tools. http:\/\/www.click2drug.org\/ . Accessed 1 Jun 2017"},{"key":"51_CR6","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.1161\/01.ATV.0000178994.21828.a7","volume":"25","author":"T Claudel","year":"2005","unstructured":"Claudel T, Staels B, Kuipers F (2005) The Farnesoid X receptor: a molecular link between bile acid and lipid and glucose metabolism. Arterioscler Thromb Vasc Biol 25:2020\u20132030","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"51_CR7","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1007\/s10822-016-9966-4","volume":"30","author":"V Salmaso","year":"2016","unstructured":"Salmaso V, Sturlese M, Cuzzolin A, Moro S (2016) DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015. J Comput Aided Mol Des 30:773\u2013789","journal-title":"J Comput Aided Mol Des"},{"key":"51_CR8","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1007\/s10822-016-9946-8","volume":"30","author":"S Gathiaka","year":"2016","unstructured":"Gathiaka S, Liu S, Chiu M et al (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":"51_CR9","doi-asserted-by":"crossref","first-page":"9977","DOI":"10.3390\/molecules20069977","volume":"20","author":"A Cuzzolin","year":"2015","unstructured":"Cuzzolin A, Sturlese M, Malvacio I, Ciancetta A, Moro S (2015) DockBench: an integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations. Molecules 20:9977\u20139993","journal-title":"Molecules"},{"key":"51_CR10","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","volume":"33","author":"PA Kollman","year":"2000","unstructured":"Kollman PA, Massova I, Reyes C et al (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":"51_CR11","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1021\/ct9000685","volume":"5","author":"MJ Harvey","year":"2009","unstructured":"Harvey MJ, Giupponi G, Fabritiis GD (2009) ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput 5:1632\u20131639","journal-title":"J Chem Theory Comput"},{"key":"51_CR12","unstructured":"Chemical Computing Group (CCG) Inc (2016) Molecular operating environment (MOE)"},{"key":"51_CR13","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/prot.22234","volume":"75","author":"P Labute","year":"2009","unstructured":"Labute P (2009) Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins 75:187\u2013205","journal-title":"Proteins"},{"key":"51_CR14","doi-asserted-by":"crossref","unstructured":"Schr\u00f6dinger (2017) Schr\u00f6dinger release 2017-1: LigPrep. New York, NY","DOI":"10.2307\/j.ctvcm4h07.62"},{"key":"51_CR15","unstructured":"RDKit: Open-source cheminformatics. http:\/\/www.rdkit.org . Accessed 28 May 2017"},{"key":"51_CR16","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1021\/ci100031x","volume":"50","author":"PCD Hawkins","year":"2010","unstructured":"Hawkins PCD, 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":"51_CR17","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1021\/jm0603365","volume":"50","author":"PCD Hawkins","year":"2007","unstructured":"Hawkins PCD, Skillman AG, Nicholls A (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem 50:74\u201382","journal-title":"J Med Chem"},{"key":"51_CR18","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","volume":"30","author":"GM Morris","year":"2009","unstructured":"Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785\u20132791","journal-title":"J Comput Chem"},{"key":"51_CR19","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739\u20131749","journal-title":"J Med Chem"},{"key":"51_CR20","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1021\/jm030644s","volume":"47","author":"TA Halgren","year":"2004","unstructured":"Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750\u20131759","journal-title":"J Med Chem"},{"key":"51_CR21","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/prot.10465","volume":"52","author":"ML Verdonk","year":"2003","unstructured":"Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein-ligand docking using GOLD. Proteins 52:609\u2013623","journal-title":"Proteins"},{"key":"51_CR22","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s11721-007-0006-9","volume":"1","author":"O Korb","year":"2007","unstructured":"Korb O, St\u00fctzle T, Exner TE (2007) An ant colony optimization approach to flexible protein\u2013ligand docking. Swarm Intell 1:115\u2013134","journal-title":"Swarm Intell"},{"key":"51_CR23","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1021\/ci800298z","volume":"49","author":"O Korb","year":"2009","unstructured":"Korb O, St\u00fctzle T, Exner TE (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model 49:84\u201396","journal-title":"J Chem Inf Model"},{"key":"51_CR24","doi-asserted-by":"crossref","first-page":"e1003571","DOI":"10.1371\/journal.pcbi.1003571","volume":"10","author":"S Ruiz-Carmona","year":"2014","unstructured":"Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, Barril X, Hubbard RE, Morley SD (2014) rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput Biol 10:e1003571","journal-title":"PLoS Comput Biol"},{"key":"51_CR25","unstructured":"Case DA, Babin V, Berryman JT, Betz RM, Cai Q, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J, Kolossv\u00e1ry I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz KM, Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Kollman PA (2014) AMBER 14. University of California, San Francisco"},{"key":"51_CR26","doi-asserted-by":"crossref","first-page":"3219","DOI":"10.1016\/0040-4020(80)80168-2","volume":"36","author":"J Gasteiger","year":"1980","unstructured":"Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity\u2014a rapid access to atomic charges. Tetrahedron 36:3219\u20133228","journal-title":"Tetrahedron"},{"key":"51_CR27","doi-asserted-by":"crossref","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":"51_CR28","doi-asserted-by":"crossref","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","journal-title":"J Chem Phys"},{"key":"51_CR29","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577","journal-title":"J Chem Phys"},{"key":"51_CR30","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","volume":"55","author":"A Onufriev","year":"2004","unstructured":"Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55:383\u2013394","journal-title":"Proteins"},{"key":"51_CR31","doi-asserted-by":"crossref","unstructured":"Weiser J, Shenkin PS, Still CW (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A"},{"key":"51_CR32","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/S1097-2765(03)00104-7","volume":"11","author":"M Downes","year":"2003","unstructured":"Downes M, Verdecia MA, Roecker AJ et al (2003) A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Mol Cell 11:1079\u20131092","journal-title":"Mol Cell"},{"key":"51_CR33","doi-asserted-by":"crossref","first-page":"5337","DOI":"10.1073\/pnas.0710981105","volume":"105","author":"SM Soisson","year":"2008","unstructured":"Soisson SM, Parthasarathy G, Adams AD, Sahoo S, Sitlani A, Sparrow C, Cui J, Becker JW (2008) Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation. Proc Natl Acad Sci USA 105:5337\u20135342","journal-title":"Proc Natl Acad Sci USA"},{"key":"51_CR34","doi-asserted-by":"crossref","first-page":"4339","DOI":"10.1016\/j.bmcl.2008.06.073","volume":"18","author":"A Akwabi-Ameyaw","year":"2008","unstructured":"Akwabi-Ameyaw A, Bass JY, Caldwell RD et al (2008) Conformationally constrained farnesoid X receptor (FXR) agonists: naphthoic acid-based analogs of GW 4064. Bioorg Med Chem Lett 18:4339\u20134343","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR35","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1021\/jm8014124","volume":"52","author":"B Flatt","year":"2009","unstructured":"Flatt B, Martin R, Wang T-L et al (2009) Discovery of XL335 (WAY-362450), a highly potent, selective, and orally active agonist of the farnesoid X receptor (FXR). J Med Chem 52:904\u2013907","journal-title":"J Med Chem"},{"key":"51_CR36","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1016\/j.bmcl.2009.03.008","volume":"19","author":"S Feng","year":"2009","unstructured":"Feng S, Yang M, Zhang Z et al (2009) Identification of an N-oxide pyridine GW4064 analog as a potent FXR agonist. Bioorg Med Chem Lett 19:2595\u20132598","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR37","doi-asserted-by":"crossref","first-page":"2969","DOI":"10.1016\/j.bmcl.2009.04.047","volume":"19","author":"JY Bass","year":"2009","unstructured":"Bass JY, Caldwell RD, Caravella JA et al (2009) Substituted isoxazole analogs of farnesoid X receptor (FXR) agonist GW4064. Bioorg Med Chem Lett 19:2969\u20132973","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR38","doi-asserted-by":"crossref","first-page":"4733","DOI":"10.1016\/j.bmcl.2009.06.062","volume":"19","author":"A Akwabi-Ameyaw","year":"2009","unstructured":"Akwabi-Ameyaw A, Bass JY, Caldwell RD et al (2009) FXR agonist activity of conformationally constrained analogs of GW 4064. Bioorg Med Chem Lett 19:4733\u20134739","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR39","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1021\/jm901650u","volume":"53","author":"JT Lundquist","year":"2010","unstructured":"Lundquist JT, Harnish DC, Kim CY et al (2010) Improvement of physiochemical properties of the tetrahydroazepinoindole series of farnesoid X receptor (FXR) agonists: beneficial modulation of lipids in primates. J Med Chem 53:1774\u20131787","journal-title":"J Med Chem"},{"key":"51_CR40","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.bmcl.2010.11.039","volume":"21","author":"HGF Richter","year":"2011","unstructured":"Richter HGF, Benson GM, Blum D et al (2011) Discovery of novel and orally active FXR agonists for the potential treatment of dyslipidemia & diabetes. Bioorg Med Chem Lett 21:191\u2013194","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR41","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1016\/j.bmcl.2010.12.123","volume":"21","author":"HGF Richter","year":"2011","unstructured":"Richter HGF, Benson GM, Bleicher KH et al (2011) Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties. Bioorg Med Chem Lett 21:1134\u20131140","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR42","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1016\/j.bmcl.2010.12.089","volume":"21","author":"JY Bass","year":"2011","unstructured":"Bass JY, Caravella JA, Chen L et al (2011) Conformationally constrained farnesoid X receptor (FXR) agonists: heteroaryl replacements of the naphthalene. Bioorg Med Chem Lett 21:1206\u20131213","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR43","doi-asserted-by":"crossref","first-page":"6154","DOI":"10.1016\/j.bmcl.2011.08.034","volume":"21","author":"A Akwabi-Ameyaw","year":"2011","unstructured":"Akwabi-Ameyaw A, Caravella JA, Chen L et al (2011) Conformationally constrained farnesoid X receptor (FXR) agonists: alternative replacements of the stilbene. Bioorg Med Chem Lett 21:6154\u20136160","journal-title":"Bioorg Med Chem Lett"},{"key":"51_CR44","doi-asserted-by":"crossref","first-page":"19888","DOI":"10.1074\/jbc.M114.630475","volume":"290","author":"X Xu","year":"2015","unstructured":"Xu X, Xu X, Liu P, Zhu Z, Chen J, Fu H, Chen L, Hu L, Shen X (2015) Structural basis for SMALL MOLECULE NDB (N-benzyl-N-(3-(tert-butyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino) benzamide) as a selective antagonist of farnesoid X receptor \u03b1 (FXR\u03b1) in stabilizing the homodimerization of the receptor. J Biol Chem 290:19888\u201319899","journal-title":"J Biol Chem"},{"key":"51_CR45","unstructured":"Kudlinzki D, Merk D, Linhard VL, Saxena K, Sreeramulu S, Nilsson E, Dekker N, Wissler L, Bamberg K, Schubert-Zsilavecz M, Schwalbe H (2015) FXR with CDCA and NCoA-2 peptide. http:\/\/www.rcsb.org\/pdb\/explore.do?structureId=4qe6 . Accessed 23 Aug 2017"},{"key":"51_CR46","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1038\/ncomms2924","volume":"4","author":"L Jin","year":"2013","unstructured":"Jin L, Feng X, Rong H et al (2013) The antiparasitic drug ivermectin is a novel FXR ligand that regulates metabolism. Nat Commun 4:1937","journal-title":"Nat Commun"},{"key":"51_CR47","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa F, Varoquaux G, Gramfort A et al (2011) Scikit-learn: machine learning in python. J Mach Learn Res 12:2825\u20132830","journal-title":"J Mach Learn Res"},{"key":"51_CR48","unstructured":"Ester M, Kriegel H-P, Sander J, Xu X (1996) A density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the 2nd international conference on knowledge discovery and data mining. Portland, OR, pp 226\u2013231"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-017-0051-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0051-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0051-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,2]],"date-time":"2019-10-02T14:59:46Z","timestamp":1570028386000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-017-0051-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,24]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1]]}},"alternative-id":["51"],"URL":"https:\/\/doi.org\/10.1007\/s10822-017-0051-4","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2017,8,24]]}}}