{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T04:31:13Z","timestamp":1774499473917,"version":"3.50.1"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,8,22]],"date-time":"2017-08-22T00:00:00Z","timestamp":1503360000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003246","name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["TOP-PUNT 718.015.001"],"award-info":[{"award-number":["TOP-PUNT 718.015.001"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["VENI 722.014.005"],"award-info":[{"award-number":["VENI 722.014.005"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["West-Life grant no. 675858"],"award-info":[{"award-number":["West-Life grant no. 675858"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["BioExcel grant no. 675728"],"award-info":[{"award-number":["BioExcel grant no. 675728"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["INDIGO-Datacloud grant no 653549"],"award-info":[{"award-number":["INDIGO-Datacloud grant no 653549"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010665","name":"H2020 Marie Sk\u0142odowska-Curie Actions","doi-asserted-by":"publisher","award":["BAP-659025"],"award-info":[{"award-number":["BAP-659025"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010665","name":"H2020 Marie Sk\u0142odowska-Curie Actions","doi-asserted-by":"publisher","award":["MEMBRANEPROT-659826"],"award-info":[{"award-number":["MEMBRANEPROT-659826"]}],"id":[{"id":"10.13039\/100010665","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\/s10822-017-0049-y","type":"journal-article","created":{"date-parts":[[2017,8,22]],"date-time":"2017-08-22T09:31:07Z","timestamp":1503394267000},"page":"175-185","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":128,"title":["Performance of HADDOCK and a simple contact-based protein\u2013ligand binding affinity predictor in the D3R Grand Challenge 2"],"prefix":"10.1007","volume":"32","author":[{"given":"Zeynep","family":"Kurkcuoglu","sequence":"first","affiliation":[]},{"given":"Panagiotis I.","family":"Koukos","sequence":"additional","affiliation":[]},{"given":"Nevia","family":"Citro","sequence":"additional","affiliation":[]},{"given":"Mikael E.","family":"Trellet","sequence":"additional","affiliation":[]},{"given":"J. P. G. L. M.","family":"Rodrigues","sequence":"additional","affiliation":[]},{"given":"Irina S.","family":"Moreira","sequence":"additional","affiliation":[]},{"given":"Jorge","family":"Roel-Touris","sequence":"additional","affiliation":[]},{"given":"Adrien S. J.","family":"Melquiond","sequence":"additional","affiliation":[]},{"given":"Cunliang","family":"Geng","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg","family":"Schaarschmidt","sequence":"additional","affiliation":[]},{"given":"Li C.","family":"Xue","sequence":"additional","affiliation":[]},{"given":"Anna","family":"Vangone","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7369-1322","authenticated-orcid":false,"given":"A. M. J. J.","family":"Bonvin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,8,22]]},"reference":[{"key":"49_CR1","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1002\/prot.22170","volume":"73","author":"N Andrusier","year":"2008","unstructured":"Andrusier N, Mashiach E, Nussinov R, Wolfson HJ (2008) Principles of flexible protein-protein docking. Proteins 73:271\u2013289","journal-title":"Proteins"},{"key":"49_CR2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules200713384","author":"LG Ferreira","year":"2015","unstructured":"Ferreira LG, Santos RN, Oliva G, Andricopulo AD (2015) Molecular docking and structure-based drug design strategies. Molecules. doi: 10.3390\/molecules200713384","journal-title":"Molecules"},{"key":"49_CR3","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.ymeth.2012.12.004","volume":"59","author":"E Karaca","year":"2013","unstructured":"Karaca E, Bonvin AMJJ (2013) Advances in integrative modeling of biomolecular complexes. Methods 59:372\u2013381","journal-title":"Methods"},{"key":"49_CR4","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1079\/9781845939434.0232","volume-title":"Antimicrob. drug Discov. Emerg. Strateg","author":"PL Kastritis","year":"2012","unstructured":"Kastritis PL, Bonvin AMJJ (2012) Predicting and dissecting high-order molecular complexity by information-driven biomolecular docking. In: Tegos A, Mylonakis E (eds) Antimicrob. drug Discov. Emerg. Strateg. CABI, Croydon, p\u00a0232"},{"key":"49_CR5","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","volume":"125","author":"C Dominguez","year":"2003","unstructured":"Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein\u2013protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731\u20131737","journal-title":"J Am Chem Soc"},{"key":"49_CR6","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1016\/j.jmb.2015.09.014","volume":"428","author":"GCP Zundert van","year":"2016","unstructured":"van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720\u2013725","journal-title":"J Mol Biol"},{"key":"49_CR7","first-page":"317","volume":"31","author":"IS Moreira","year":"2010","unstructured":"Moreira IS, Fernandes PA, Ramos MJ (2010) Protein-protein docking dealing with the unknown. J Comput Chem 31:317\u2013342","journal-title":"J Comput Chem"},{"key":"49_CR8","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1002\/prot.25198","volume":"85","author":"A Vangone","year":"2017","unstructured":"Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ (2017) Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins Struct Funct Bioinform 85:417\u2013423","journal-title":"Proteins Struct Funct Bioinform"},{"key":"49_CR9","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1002\/prot.10381","volume":"52","author":"J Janin","year":"2003","unstructured":"Janin J, Henrick K, Moult J, ten Eyck L, Sternberg MJE, Vajda S, Vakser I, Wodak SJ (2003) CAPRI: a critical assessment of PRedicted interactions. Proteins 52:2\u20139","journal-title":"Proteins"},{"key":"49_CR10","doi-asserted-by":"crossref","first-page":"7071","DOI":"10.1073\/pnas.0509392103","volume":"103","author":"L Rutten","year":"2006","unstructured":"Rutten L, Geurtsen J, Lambert W, Smolenaers JJM, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J (2006) Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Proc Natl Acad Sci 103:7071\u20137076","journal-title":"Proc Natl Acad Sci"},{"key":"49_CR11","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1002\/prot.21517","volume":"69","author":"S Tomaselli","year":"2007","unstructured":"Tomaselli S, Ragona L, Zetta L, Assfalg M, Ferranti P, Longhi R, Bonvin AMJJ, Molinari H (2007) NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids. Proteins 69:177\u2013191","journal-title":"Proteins"},{"key":"49_CR12","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/glycob\/cwl062","volume":"17","author":"AM Wu","year":"2007","unstructured":"Wu AM, Singh T, Liu J-H, Krzeminski M, Russwurm R, Siebert H-C, Bonvin AMJJ, Andre S, Gabius H-J (2007) Activity-structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16. Glycobiology 17:165\u2013184","journal-title":"Glycobiology"},{"key":"49_CR13","doi-asserted-by":"crossref","first-page":"12661","DOI":"10.1021\/bi801597b","volume":"47","author":"CJ Arnusch","year":"2008","unstructured":"Arnusch CJ, Bonvin AMJJ, Verel AM, Jansen WTM, Liskamp RMJ, de Kruijff B, Pieters RJ, Breukink E (2008) The vancomycin\u2013nisin(1\u201312) hybrid restores activity against vancomycin resistant enterococci. BioChemistry 47:12661\u201312663","journal-title":"BioChemistry"},{"key":"49_CR14","doi-asserted-by":"crossref","first-page":"1960","DOI":"10.1073\/pnas.0813064106","volume":"106","author":"L Rutten","year":"2009","unstructured":"Rutten L, Mannie J-PBA, Stead CM, Raetz CRH, Reynolds CM, Bonvin AMJJ, Tommassen JP, Egmond MR, Trent MS, Gros P (2009) Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium. Proc Natl Acad Sci USA 106:1960\u20131964","journal-title":"Proc Natl Acad Sci USA"},{"key":"49_CR15","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1126\/science.1185723","volume":"328","author":"T Schneider","year":"2010","unstructured":"Schneider T, Kruse T, Wimmer R, Wiedemann I, Sass V, Pag U, Jansen A, Nielsen AK, Mygind PH, Raventos DS, Neve S, Ravn B, Bonvin AMJJ, De Maria L, Andersen AS, Gammelgaard LK, Sahl H-G, Kristensen H-H (2010) Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science 328:1168\u20131172","journal-title":"Science"},{"key":"49_CR16","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1021\/ci4005332","volume":"54","author":"PL Kastritis","year":"2014","unstructured":"Kastritis PL, Rodrigues JPGLM, Bonvin AMJJ (2014) HADDOCK2P2I: a biophysical model for predicting the binding affinity of protein\u2013protein interaction inhibitors. J Chem Inf Model 54:826\u2013836","journal-title":"J Chem Inf Model"},{"key":"49_CR17","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1002\/cbic.201700059","volume":"18","author":"W Zheng","year":"2017","unstructured":"Zheng W, Lu Y, Lin S, Wang R, Qiu L, Zhu Y, Yao B, Guo F, Jin S, Jin L, Li Y (2017) A novel class of natural FXR modulators with a unique mode of selective co-regulator assembly. ChemBioChem 18:721\u2013725","journal-title":"ChemBioChem"},{"key":"49_CR18","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.apsb.2015.01.004","volume":"5","author":"L Ding","year":"2015","unstructured":"Ding L, Yang L, Wang Z, Huang W (2015) Bile acid nuclear receptor FXR and digestive system diseases. Acta Pharm Sin B 5:135\u2013144","journal-title":"Acta Pharm Sin B"},{"key":"49_CR19","first-page":"5","volume":"3","author":"AH Ali","year":"2015","unstructured":"Ali AH, Carey EJ, Lindor KD (2015) Recent advances in the development of farnesoid X receptor agonists. Ann Transl Med 3:5","journal-title":"Ann Transl Med"},{"key":"49_CR20","unstructured":"(2017) Omega Toolkit 2.6.4 OpenEye Scientific Software. Santa Fe, NM"},{"key":"49_CR21","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.jmgm.2003.12.005","volume":"22","author":"M Feig","year":"2004","unstructured":"Feig M, Karanicolas J, Brooks CL 3rd (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22:377\u2013395","journal-title":"J Mol Graph Model"},{"key":"49_CR22","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":"49_CR23","unstructured":"Hubbard S, Thornton J (1993) NACCESS, computer program, department of biochemistry molecular biology. University College London"},{"key":"49_CR24","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1107\/S0567739482001806","volume":"38","author":"AD McLachlan","year":"1982","unstructured":"McLachlan AD (1982) Rapid comparison of protein structures. Acta Crystallogr Sect A 38:871\u2013873","journal-title":"Acta Crystallogr Sect A"},{"key":"49_CR25","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1002\/(SICI)1521-3773(19990115)38:1\/2<236::AID-ANIE236>3.0.CO;2-M","volume":"38","author":"X Daura","year":"1999","unstructured":"Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE (1999) Peptide folding: when simulation meets experiment. Angew Chemie Int Ed 38:236\u2013240","journal-title":"Angew Chemie Int Ed"},{"key":"49_CR26","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1016\/S1097-2765(03)00112-6","volume":"11","author":"L-Z Mi","year":"2003","unstructured":"Mi L-Z, Devarakonda S, Harp JM, Han Q, Pellicciari R, Willson TM, Khorasanizadeh S, Rastinejad F (2003) Structural basis for bile acid binding and activation of the nuclear receptor FXR. Mol Cell 11:1093\u20131100","journal-title":"Mol Cell"},{"key":"49_CR27","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, Creech KL, Deaton DN, Madauss KP, Marr HB, McFadyen RB, Miller AB, Mills WY, Navas F 3rd, Parks DJ, Smalley TLJ, Spearing PK, Todd D, Williams SP, Wisely GB (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":"49_CR28","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, Caravella JA, Chen L, Creech KL, Deaton DN, Jones SA, Kaldor I, Liu Y, Madauss KP, Marr HB, McFadyen RB, Miller AB, Navas FIII, Parks DJ, Spearing PK, Todd D, Williams SP, Wisely GB (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":"49_CR29","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, Blum D, Chaput E, Clemann N, Feng S, Gardes C, Grether U, Hartman P, Kuhn B, Martin RE, Plancher J-M, Rudolph MG, Schuler F, Taylor S (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":"49_CR30","unstructured":"The PyMOL molecular graphics system, Version 1.8. Schr\u00f6dinger, LLC,"},{"key":"49_CR31","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1093\/bioinformatics\/btt475","volume":"29","author":"Y Wang","year":"2013","unstructured":"Wang Y, Backman TWH, Horan K, Girke T (2013) fmcsR: mismatch tolerant maximum common substructure searching in R. Bioinformatics 29:2792\u20132794","journal-title":"Bioinformatics"},{"key":"49_CR32","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/bioinformatics\/btn307","volume":"24","author":"Y Cao","year":"2008","unstructured":"Cao Y, Charisi A, Cheng L-C, Jiang T, Girke T (2008) ChemmineR: a compound mining framework for R. Bioinformatics 24:1733","journal-title":"Bioinformatics"},{"key":"49_CR33","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1002\/prot.10232","volume":"49","author":"JWM Nissink","year":"2002","unstructured":"Nissink JWM, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R (2002) A new test set for validating predictions of protein\u2013ligand interaction. Proteins Struct Funct Bioinforma 49:457\u2013471","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"49_CR34","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, Caravella JA, Chen L, Creech KL, Deaton DN, Madauss KP, Marr HB, McFadyen RB, Miller AB, Navas F 3rd, Parks DJ, Spearing PK, Todd D, Williams SP, Bruce Wisely G (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":"49_CR35","first-page":"1355","volume":"D60","author":"AW Sch\u00fcttelkopf","year":"2004","unstructured":"Sch\u00fcttelkopf AW, van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D60:1355\u20131363","journal-title":"Acta Crystallogr"},{"key":"49_CR36","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/j.jmb.2003.10.069","volume":"335","author":"J Fernandez-Recio","year":"2004","unstructured":"Fernandez-Recio J, Totrov M, Abagyan R (2004) Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335:843\u2013865","journal-title":"J Mol Biol"},{"key":"49_CR37","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1021\/ja00214a001","volume":"110","author":"WL Jorgensen","year":"1988","unstructured":"Jorgensen WL, Tirado-Rives J (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657\u20131666","journal-title":"J Am Chem Soc"},{"key":"49_CR38","doi-asserted-by":"crossref","first-page":"D1045","DOI":"10.1093\/nar\/gkv1072","volume":"44","author":"MK Gilson","year":"2016","unstructured":"Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J (2016) BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res 44:D1045","journal-title":"Nucleic Acids Res"},{"key":"49_CR39","first-page":"27","volume":"2","author":"C-C Chang","year":"2011","unstructured":"Chang C-C, Lin C-J (2011) LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2:27","journal-title":"ACM Trans Intell Syst Technol"},{"key":"49_CR40","doi-asserted-by":"crossref","first-page":"e07454","DOI":"10.7554\/eLife.07454","volume":"4","author":"A Vangone","year":"2015","unstructured":"Vangone A, Bonvin AMJJ (2015) Contacts-based prediction of binding affinity in protein\u2013protein complexes. Elife 4:e07454","journal-title":"Elife"},{"key":"49_CR41","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1093\/bioinformatics\/btw514","volume":"32","author":"LC Xue","year":"2016","unstructured":"Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A (2016) PRODIGY: a web server for predicting the binding affinity of protein\u2013protein complexes. Bioinformatics 32:3676\u20133678","journal-title":"Bioinformatics"},{"key":"49_CR42","doi-asserted-by":"crossref","first-page":"e2124","DOI":"10.21769\/BioProtoc.2124","volume":"7","author":"A Vangone","year":"2017","unstructured":"Vangone A, Bonvin AMJJ (2017) PRODIGY: a contact-based predictor of binding affinity in protein\u2013protein complexes. Bio-protocol 7:e2124","journal-title":"Bio-protocol"},{"key":"49_CR43","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1002\/pro.580","volume":"20","author":"PL Kastritis","year":"2011","unstructured":"Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AMJJ, Janin J (2011) A structure-based benchmark for protein\u2013protein binding affinity. Protein Sci 20:482\u2013491","journal-title":"Protein Sci"},{"key":"49_CR44","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1016\/j.jmb.2015.07.016","volume":"427","author":"T Vreven","year":"2015","unstructured":"Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jim\u00e9nez-Garc\u00eda B, Bates PA, Fernandez-Recio J, Bonvin AMJJ, Weng Z (2015) Updates to the integrated protein\u2013protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2. J Mol Biol 427:3031\u20133041","journal-title":"J Mol Biol"},{"key":"49_CR45","unstructured":"R Core Team (2016) R: a language and environment for statistical computing"},{"key":"49_CR46","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1021\/ci100335w","volume":"50","author":"JA Lemkul","year":"2010","unstructured":"Lemkul JA, Allen WJ, Bevan DR (2010) Practical considerations for building GROMOS-compatible small-molecule topologies. J Chem Inf Model 50:2221\u20132235","journal-title":"J Chem Inf Model"},{"key":"49_CR47","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1186\/1756-0500-5-367","volume":"5","author":"AW Silva da","year":"2012","unstructured":"da Silva AW, Vranken WF (2012) ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res Notes 5:367","journal-title":"BMC Res Notes"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-017-0049-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0049-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-017-0049-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T05:28:44Z","timestamp":1692941324000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-017-0049-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,22]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1]]}},"alternative-id":["49"],"URL":"https:\/\/doi.org\/10.1007\/s10822-017-0049-y","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,22]]}}}