{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:17:37Z","timestamp":1778635057695,"version":"3.51.4"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,3,16]],"date-time":"2018-03-16T00:00:00Z","timestamp":1521158400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["1316053"],"award-info":[{"award-number":["1316053"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["4689\/2-1"],"award-info":[{"award-number":["4689\/2-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007215","name":"Verband der Chemischen Industrie","doi-asserted-by":"publisher","award":["199200"],"award-info":[{"award-number":["199200"]}],"id":[{"id":"10.13039\/100007215","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Mercator Research Center Ruhr","award":["AN-2015-0053"],"award-info":[{"award-number":["AN-2015-0053"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s13321-018-0264-0","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T00:52:02Z","timestamp":1522803122000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening"],"prefix":"10.1186","volume":"10","author":[{"given":"Julia B.","family":"Jasper","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3151-9158","authenticated-orcid":false,"given":"Lina","family":"Humbeck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6272-4456","authenticated-orcid":false,"given":"Tobias","family":"Brinkjost","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9228-217X","authenticated-orcid":false,"given":"Oliver","family":"Koch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,3,16]]},"reference":[{"issue":"16","key":"264_CR1","doi-asserted-by":"publisher","first-page":"1923","DOI":"10.2174\/1568026614666140929124445","volume":"14","author":"E Lionta","year":"2014","unstructured":"Lionta E, Spyrou G, Vassilatis DK, Cournia Z (2014) Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem 14(16):1923\u20131938","journal-title":"Curr Top Med Chem"},{"key":"264_CR2","doi-asserted-by":"publisher","first-page":"12899","DOI":"10.1039\/c0cp00151a","volume":"12","author":"SY Huang","year":"2010","unstructured":"Huang SY, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein\u2013ligand docking: recent advances and future directions. Phys Chem Chem Phys 12:12899\u201312908","journal-title":"Phys Chem Chem Phys"},{"issue":"11","key":"264_CR3","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nrd1549","volume":"3","author":"DB Kitchen","year":"2004","unstructured":"Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935\u2013949","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"264_CR4","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1007\/s12551-013-0130-2","volume":"6","author":"IA Guedes","year":"2014","unstructured":"Guedes IA, de Magalh\u00e3es CS, Dardenne LE (2014) Receptor-ligand molecular docking. Biophys Rev 6(1):75\u201387","journal-title":"Biophys Rev"},{"key":"264_CR5","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.1021\/acs.jmedchem.6b01437","volume":"60","author":"Y Hu","year":"2016","unstructured":"Hu Y, Stumpfe D, Bajorath J (2016) Recent advances in scaffold hopping. J Med Chem 60:1238\u20131246","journal-title":"J Med Chem"},{"issue":"19","key":"264_CR6","doi-asserted-by":"publisher","first-page":"2894","DOI":"10.1002\/(SICI)1521-3773(19991004)38:19<2894::AID-ANIE2894>3.0.CO;2-F","volume":"38","author":"G Schneider","year":"1999","unstructured":"Schneider G, Neidhart W, Giller T, Schmid G (1999) \u201cScaffold-Hopping\u201d by topological pharmacophore search: a contribution to virtual screening. Angew Chem Int Ed 38(19):2894\u20132896","journal-title":"Angew Chem Int Ed"},{"issue":"11","key":"264_CR7","doi-asserted-by":"publisher","first-page":"3222","DOI":"10.1021\/jm8001058","volume":"51","author":"J Venhorst","year":"2008","unstructured":"Venhorst J, N\u00fa\u00f1ez S, Terpstra JW, Kruse CG (2008) Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints. J Med Chem 51(11):3222\u20133229","journal-title":"J Med Chem"},{"key":"264_CR8","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1002\/9783527665143.ch14","volume-title":"Scaffold hopping in medicinal chemistry","author":"D Rognan","year":"2013","unstructured":"Rognan D, Desaphy J (2013) Molecular interaction fingerprints. In: Brown N (ed) Scaffold hopping in medicinal chemistry, 1st edn. Wiley-VCH Verlag GmbH & Co KGaA, Weinheim, pp 215\u2013230","edition":"1"},{"issue":"2","key":"264_CR9","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1021\/jm030331x","volume":"47","author":"Z Deng","year":"2004","unstructured":"Deng Z, Chuaqui C, Singh J (2004) Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein\u2013ligand binding interactions. J Med Chem 47(2):337\u2013344","journal-title":"J Med Chem"},{"issue":"1","key":"264_CR10","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1021\/jm049312t","volume":"48","author":"C Chuaqui","year":"2005","unstructured":"Chuaqui C, Deng Z, Singh J (2005) Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J Med Chem 48(1):121\u2013133","journal-title":"J Med Chem"},{"issue":"5","key":"264_CR11","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1021\/ci800466n","volume":"49","author":"RK Nandigam","year":"2009","unstructured":"Nandigam RK, Kim S, Singh J, Chuaqui C (2009) Position specific interaction dependent scoring technique for virtual screening based on weighted protein\u2013ligand interaction fingerprint profiles. J Chem Inf Model 49(5):1185\u20131192","journal-title":"J Chem Inf Model"},{"issue":"1","key":"264_CR12","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1021\/ci600342e","volume":"47","author":"G Marcou","year":"2007","unstructured":"Marcou G, Rognan D (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 47(1):195\u2013207","journal-title":"J Chem Inf Model"},{"issue":"6","key":"264_CR13","first-page":"1942","volume":"44","author":"MD Kelly","year":"2004","unstructured":"Kelly MD, Mancera RL (2004) Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design. J Chem Inf Model 44(6):1942\u20131951","journal-title":"J Chem Inf Model"},{"issue":"2","key":"264_CR14","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1021\/ci050420d","volume":"46","author":"CP Mpamhanga","year":"2006","unstructured":"Mpamhanga CP, Chen B, McLay IM, Willett P (2006) Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions. J Chem Inf Model 46(2):686\u2013698","journal-title":"J Chem Inf Model"},{"issue":"9","key":"264_CR15","doi-asserted-by":"publisher","first-page":"2555","DOI":"10.1021\/ci500319f","volume":"54","author":"C Da","year":"2014","unstructured":"Da C, Kireev D (2014) Structural protein\u2013ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study. J Chem Inf Model 54(9):2555\u20132561","journal-title":"J Chem Inf Model"},{"issue":"5","key":"264_CR16","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1021\/ci900043r","volume":"49","author":"VI Perez-Nueno","year":"2009","unstructured":"Perez-Nueno VI, Rabal O, Borrell JI, Teixido J (2009) APIF: a new interaction fingerprint based on atom pairs and Its application to virtual screening. J Chem Inf Model 49(5):1245\u20131260","journal-title":"J Chem Inf Model"},{"issue":"3","key":"264_CR17","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1021\/ci300566n","volume":"53","author":"J Desaphy","year":"2013","unstructured":"Desaphy J, Raimbaud E, Ducrot P, Rognan D (2013) Encoding protein\u2013ligand interaction patterns in fingerprints and graphs. J Chem Inf Model 53(3):623\u2013637","journal-title":"J Chem Inf Model"},{"key":"264_CR18","doi-asserted-by":"publisher","first-page":"6789","DOI":"10.1021\/jm0608356","volume":"49","author":"N Huang","year":"2006","unstructured":"Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789\u20136801","journal-title":"J Med Chem"},{"key":"264_CR19","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"G Jones","year":"1997","unstructured":"Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727\u2013748","journal-title":"J Mol Biol"},{"key":"264_CR20","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1021\/ci600471m","volume":"47","author":"G Carta","year":"2007","unstructured":"Carta G, Knox AJS, Lloyd DG (2007) Unbiasing scoring functions: a new normalization and rescoring strategy. J Chem Inf Model 47:1564\u20131571","journal-title":"J Chem Inf Model"},{"key":"264_CR21","doi-asserted-by":"publisher","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\u2013ligand docking with PLANTS. J Chem Inf Model 49:84\u201396","journal-title":"J Chem Inf Model"},{"issue":"6","key":"264_CR22","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.1021\/ci500081m","volume":"54","author":"Y Li","year":"2014","unstructured":"Li Y, Han L, Liu Z, Wang R (2014) Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results. J Chem Inf Model 54(6):1717\u20131736","journal-title":"J Chem Inf Model"},{"key":"264_CR23","unstructured":"CCDC (2017) GOLD scoring function performance against the DUD decoy\/active set. \n                    https:\/\/www.ccdc.cam.ac.uk\/support-and-resources\/ccdcresources\/VS_workcase.pdf\n                    \n                  . Accessed 27 Sept 2017"},{"issue":"4","key":"264_CR24","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1021\/jm061277y","volume":"50","author":"MJ Hartshorn","year":"2007","unstructured":"Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN et al (2007) Diverse, high-quality test set for the validation of protein\u2013ligand docking performance. J Med Chem 50(4):726\u2013741","journal-title":"J Med Chem"},{"key":"264_CR25","doi-asserted-by":"publisher","first-page":"3315","DOI":"10.1021\/jm051197e","volume":"49","author":"R Thomsen","year":"2006","unstructured":"Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49:3315\u20133321","journal-title":"J Med Chem"},{"issue":"6","key":"264_CR26","doi-asserted-by":"publisher","first-page":"1455","DOI":"10.1021\/ci900056c","volume":"49","author":"JB Cross","year":"2009","unstructured":"Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y et al (2009) Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 49(6):1455\u20131474","journal-title":"J Chem Inf Model"},{"issue":"4","key":"264_CR27","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1021\/jm020406h","volume":"46","author":"AN Jain","year":"2003","unstructured":"Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46(4):499\u2013511","journal-title":"J Med Chem"},{"issue":"1","key":"264_CR28","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.bmc.2005.08.010","volume":"14","author":"E Anagnostou","year":"2006","unstructured":"Anagnostou E, Kosmopoulou MN, Chrysina ED, Leonidas DD, Hadjiloi T, Tiraidis C et al (2006) Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-d-glucopyranosylamine and N-trifluoroacetyl-beta-d-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase. Bioorgan Med Chem 14(1):181\u2013189","journal-title":"Bioorgan Med Chem"},{"issue":"9","key":"264_CR29","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/nrd2092","volume":"5","author":"B Turk","year":"2006","unstructured":"Turk B (2006) Targeting proteases: successes, failures and future prospects. Nat Rev Drug Discov 5(9):785\u2013799","journal-title":"Nat Rev Drug Discov"},{"issue":"5","key":"264_CR30","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/S0969-2126(97)00216-5","volume":"15","author":"A Urzhumtsev","year":"1997","unstructured":"Urzhumtsev A, T\u00eate-Favier F, Mitschler A, Barbanton J, Barth P, Urzhumtseva L et al (1997) A \u201cspecificity\u201d pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure\u00a015(5):601\u2013612","journal-title":"Structure"},{"issue":"May","key":"264_CR31","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1126\/science.276.5314.955","volume":"276","author":"M Mohammadi","year":"1997","unstructured":"Mohammadi M, McMahon G, Sun L, Tang C, Hirth P, Yeh BK et al (1997) Structures of the tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors. Science 276(May):955\u2013960","journal-title":"Science"},{"issue":"14","key":"264_CR32","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1021\/jm0300173","volume":"46","author":"M Schapira","year":"2003","unstructured":"Schapira M, Abagyan R, Totrov M (2003) Nuclear hormone receptor targeted virtual screening. J Med Chem 46(14):3045\u20133059","journal-title":"J Med Chem"},{"issue":"5","key":"264_CR33","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1021\/ci200515g","volume":"52","author":"A Nurisso","year":"2012","unstructured":"Nurisso A, Bravo J, Carrupt PA, Daina A (2012) Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance. J Chem Inf Model 52(5):1319\u20131327","journal-title":"J Chem Inf Model"},{"issue":"1","key":"264_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13321-017-0213-3","volume":"9","author":"T Sch\u00e4fer","year":"2017","unstructured":"Sch\u00e4fer T, Kriege N, Humbeck L, Klein K, Koch O, Mutzel P (2017) Scaffold Hunter: a comprehensive visual analytics framework for drug discovery. J Cheminform 9(1):1\u201318","journal-title":"J Cheminform"},{"key":"264_CR35","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1021\/ci100050t","volume":"50","author":"D Rogers","year":"2010","unstructured":"Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742\u2013754","journal-title":"J Chem Inf Model"},{"key":"264_CR36","unstructured":"Pipeline Pilot (2016) Dassault Syst\u00e8mes BIOVIA, discovery studio modelling environment, Release 2016, San Diego"},{"issue":"1","key":"264_CR37","doi-asserted-by":"publisher","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 et al (2000) The protein data bank. Nucleic Acids Res 28(1):235\u2013242","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"264_CR38","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1093\/bioinformatics\/btr055","volume":"27","author":"G Neudert","year":"2011","unstructured":"Neudert G, Klebe G (2011) fconv: format conversion, manipulation and feature computation of molecular data. Bioinformatics 27(7):1021\u20131022","journal-title":"Bioinformatics"},{"key":"264_CR39","unstructured":"Molecular Operating Environment (MOE) (2018) 2013.08. 1010 Sherbooke St. West, Suite #910, Montreal, QC, H3A 2R7, Canada: Chemical Computing Group ULC. \n                    http:\/\/www.chemcomp.com\/index.htm"},{"key":"264_CR40","doi-asserted-by":"crossref","unstructured":"Berthold MR, Cebron N, Dill F, Gabriel TR, K\u00f6tter T, Meinl T et al (2008) KNIME: the konstanz information miner. In: Preisach C, Burkhardt H, Schmidt-Thieme L, Decker R (eds) Data analysis, machine learning and applications. Studies in classification, data analysis, and knowledge organization. Springer, Berlin","DOI":"10.1007\/978-3-540-78246-9_38"},{"issue":"13","key":"264_CR41","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC et al (2004) UCSF Chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605\u20131612","journal-title":"J Comput Chem"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-018-0264-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13321-018-0264-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-018-0264-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,23]],"date-time":"2019-09-23T03:46:05Z","timestamp":1569210365000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-018-0264-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3,16]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["264"],"URL":"https:\/\/doi.org\/10.1186\/s13321-018-0264-0","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,16]]},"assertion":[{"value":"9 May 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 March 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"15"}}