{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T17:36:36Z","timestamp":1767893796816,"version":"3.49.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2016,3,1]],"date-time":"2016-03-01T00:00:00Z","timestamp":1456790400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2016,3,1]],"date-time":"2016-03-01T00:00:00Z","timestamp":1456790400000},"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"],"published-print":{"date-parts":[[2016,3]]},"DOI":"10.1007\/s10822-016-9906-3","type":"journal-article","created":{"date-parts":[[2016,3,5]],"date-time":"2016-03-05T09:34:48Z","timestamp":1457170488000},"page":"191-208","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Lessons learned from the design of chemical space networks and opportunities for new applications"],"prefix":"10.1007","volume":"30","author":[{"given":"Martin","family":"Vogt","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dagmar","family":"Stumpfe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerald M.","family":"Maggiora","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00fcrgen","family":"Bajorath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,3,5]]},"reference":[{"key":"9906_CR1","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1038\/nature03192","volume":"432","author":"C Dobson","year":"2004","unstructured":"Dobson C (2004) Chemical space and biology. Nature 432:824\u2013828","journal-title":"Nature"},{"key":"9906_CR2","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1007\/s10822-014-9760-0","volume":"28","author":"GM Maggiora","year":"2014","unstructured":"Maggiora GM, Bajorath J (2014) Chemical space networks\u2014a powerful new paradigm for the description of chemical space. J Comput Aided Mol Des 28:795\u2013802","journal-title":"J Comput Aided Mol Des"},{"key":"9906_CR3","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/s10822-014-9821-4","volume":"29","author":"M Zwierzyna","year":"2015","unstructured":"Zwierzyna M, Vogt M, Maggiora GM, Bajorath J (2015) Design and characterization of chemical space networks for different compound data sets. J Comput Aided Mol Des 29:113\u2013125","journal-title":"J Comput Aided Mol Des"},{"key":"9906_CR4","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1007\/s10822-015-9852-5","volume":"29","author":"B Zhang","year":"2015","unstructured":"Zhang B, Vogt M, Maggiora GM, Bajorath J (2015) Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity. J Comput Aided Mol Des 29:595\u2013608","journal-title":"J Comput Aided Mol Des"},{"key":"9906_CR5","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1007\/s10822-015-9872-1","volume":"29","author":"B Zhang","year":"2015","unstructured":"Zhang B, Vogt M, Maggiora GM, Bajorath J (2015) Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. J Comput Aided Mol Des 29:937\u2013950","journal-title":"J Comput Aided Mol Des"},{"key":"9906_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10822-015-9891-y","volume":"30","author":"M Wu","year":"2016","unstructured":"Wu M, Vogt M, Maggiora GM, Bajorath J (2016) Design of chemical space networks on the basis of Tversky similarity. J Comput Aided Mol Des 30:1\u201312","journal-title":"J Comput Aided Mol Des"},{"key":"9906_CR7","doi-asserted-by":"publisher","first-page":"6075","DOI":"10.1021\/jm800867g","volume":"51","author":"M Wawer","year":"2008","unstructured":"Wawer M, Peltason L, Weskamp N, Teckentrup A, Bajorath J (2008) Structure\u2013activity relationship anatomy by network-like similarity graphs and local structure\u2013activity relationship indices. J Med Chem 51:6075\u20136084","journal-title":"J Med Chem"},{"key":"9906_CR8","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1021\/ci900123v","volume":"49","author":"N Tanaka","year":"2009","unstructured":"Tanaka N, Ohno K, Niimi T, Moritomo A, Mori K, Orita M (2009) Small-world phenomena in chemical library networks: application to fragment-based drug discovery. J Chem Inf Model 49:2677\u20132686","journal-title":"J Chem Inf Model"},{"key":"9906_CR9","doi-asserted-by":"publisher","first-page":"12905","DOI":"10.1021\/jp204022u","volume":"115","author":"MP Krein","year":"2011","unstructured":"Krein MP, Sukumar N (2011) Exploration of the topology of chemical spaces with network measures. J Phys Chem A 115:12905\u201312918","journal-title":"J Phys Chem A"},{"key":"9906_CR10","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1002\/minf.201300076","volume":"32","author":"D Fourches","year":"2013","unstructured":"Fourches D, Tropsha A (2013) Using graph indices for the analysis and comparison of chemical data sets. Mol Inf 32:827\u2013842","journal-title":"Mol Inf"},{"key":"9906_CR11","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1021\/ci400728r","volume":"54","author":"D Stumpfe","year":"2014","unstructured":"Stumpfe D, Dimova D, Bajorath J (2014) Composition and topology of activity cliff clusters formed by bioactive compounds. J Chem Inf Model 54:451\u2013461","journal-title":"J Chem Inf Model"},{"key":"9906_CR12","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199206650.001.0001","volume-title":"Networks\u2014an introduction","author":"M Newman","year":"2010","unstructured":"Newman M (2010) Networks\u2014an introduction. Oxford University Press Inc., New York"},{"key":"9906_CR13","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1146\/annurev.soc.27.1.415","volume":"27","author":"M McPherson","year":"2001","unstructured":"McPherson M, Smith-Lovin L, Cook J (2001) Birds of a feather: homophily in social networks. Annu Rev Sociol 27:415\u2013444","journal-title":"Annu Rev Sociol"},{"key":"9906_CR14","volume-title":"Concepts and applications of molecular similarity","year":"1990","unstructured":"Johnson M, Maggiora GM (eds) (1990) Concepts and applications of molecular similarity. Wiley, New York"},{"key":"9906_CR15","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1002\/spe.4380211102","volume":"21","author":"TMJ Fruchterman","year":"1991","unstructured":"Fruchterman TMJ, Reingold EM (1991) Graph drawing by force-directed placement. Softw Pract Exp 21:1129\u20131164","journal-title":"Softw Pract Exp"},{"key":"9906_CR16","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"AJ Enright","year":"2002","unstructured":"Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575\u20131584","journal-title":"Nucleic Acids Res"},{"key":"9906_CR17","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":"9906_CR18","volume-title":"Chemoinformatics\u2014concepts, methods, and tools for drug discovery","author":"GM Maggiora","year":"2004","unstructured":"Maggiora GM, Shanmugasundaram V (2004) Molecular similarity measures. In: Bajorath J (ed) Chemoinformatics\u2014concepts, methods, and tools for drug discovery. Humana Press, Totowa"},{"key":"9906_CR19","doi-asserted-by":"crossref","unstructured":"Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40(Database issue):D1100\u2013D1107","DOI":"10.1093\/nar\/gkr777"},{"key":"9906_CR20","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/BF02294245","volume":"50","author":"GW Milligan","year":"1985","unstructured":"Milligan GW, Cooper MC (1985) An examination of procedures for determining the number of clusters in a data set. Psychometrika 50:159\u2013179","journal-title":"Psychometrika"},{"key":"9906_CR21","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1021\/ci990086j","volume":"40","author":"DJ Wild","year":"2000","unstructured":"Wild DJ, Blankley CJ (2000) Comparison of 2D fingerprint types and hierarchy level selection methods for structural grouping using Ward\u2019s clustering. J Chem Inf Comput Sci 40:155\u2013162","journal-title":"J Chem Inf Comput Sci"},{"key":"9906_CR22","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"JJ Irwin","year":"2012","unstructured":"Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52:1757\u20131768","journal-title":"J Chem Inf Model"},{"key":"9906_CR23","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1002\/3527603743.ch11","volume-title":"Chemoinformatics in drug discovery","author":"PW Kenny","year":"2005","unstructured":"Kenny PW, Sadowski J (2005) Structure modification in chemical databases. In: Oprea TI (ed) Chemoinformatics in drug discovery. Wiley-VCH, Weinheim, pp 271\u2013285"},{"key":"9906_CR24","doi-asserted-by":"publisher","first-page":"e0002051","DOI":"10.1371\/journal.pone.0002051","volume":"3","author":"M Humphries","year":"2008","unstructured":"Humphries M, Gurney K (2008) Network \u2018small-world-ness\u2018: a quantitative method for determining canonical network equivalence. PLoS ONE 3:e0002051","journal-title":"PLoS ONE"},{"key":"9906_CR25","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199211517.001.0001","volume-title":"Scale-free networks","author":"G Caldarelli","year":"2007","unstructured":"Caldarelli G (2007) Scale-free networks. Oxford University Press, Oxford"},{"key":"9906_CR26","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1021\/ci060117s","volume":"46","author":"GM Maggiora","year":"2006","unstructured":"Maggiora GM (2006) On outliers and activity cliffs\u2014why QSAR often disappoints. J Chem Inf Model 46:1535","journal-title":"J Chem Inf Model"},{"key":"9906_CR27","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1021\/jm401120g","volume":"57","author":"D Stumpfe","year":"2014","unstructured":"Stumpfe D, Hu Y, Dimova D, Bajorath J (2014) Recent progress in understanding activity cliffs and their utility in medicinal chemistry. J Med Chem 57:18\u201328","journal-title":"J Med Chem"},{"key":"9906_CR28","first-page":"1","volume-title":"Foodinformatics\u2014applications of chemical information to food chemistry","author":"GM Maggiora","year":"2014","unstructured":"Maggiora GM (2014) Introduction to molecular similarity and chemical space. In: Martinez-Mayorga K, Medina-Franco JL (eds) Foodinformatics\u2014applications of chemical information to food chemistry. Springer, Heidelberg, pp 1\u201381"},{"key":"9906_CR29","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1038\/nbt1338","volume":"25","author":"MA Yildirim","year":"2007","unstructured":"Yildirim MA, Goh K-I, Cusick ME, Barab\u00e1si A-L, Vidal M (2007) Drug-target network. Nat Biotech 25:1119\u20131126","journal-title":"Nat Biotech"},{"key":"9906_CR30","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1142\/9789812772367_0005","volume-title":"Biological Networks","author":"K Tan","year":"2007","unstructured":"Tan K, Ideker T (2007) Protein interaction networks. In: K\u00e9p\u00e8s F (ed) Biological Networks. World Scientific, Singapore, pp 133\u2013161"},{"key":"9906_CR31","doi-asserted-by":"publisher","first-page":"2944","DOI":"10.1021\/jm200026b","volume":"54","author":"M Wawer","year":"2011","unstructured":"Wawer M, Bajorath J (2011) Local structural changes, global data views: graphical substructure\u2013activity relationship trailing. J Med Chem 54:2944\u20132951","journal-title":"J Med Chem"},{"key":"9906_CR32","volume-title":"Information theory\u2014structural models for qualitative data","author":"K Krippendorff","year":"1986","unstructured":"Krippendorff K (1986) Information theory\u2014structural models for qualitative data. Sage Publications, Newbury Park"},{"key":"9906_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10910-005-4525-6","volume":"38","author":"GM Maggiora","year":"2005","unstructured":"Maggiora GM, Shanmugasundaram V (2005) An information-theoretic characterization of partitioned property spaces. J Math Chem 38:1\u201320","journal-title":"J Math Chem"},{"key":"9906_CR34","volume-title":"Information theory and molecular biology","author":"HP Yockey","year":"1992","unstructured":"Yockey HP (1992) Information theory and molecular biology. Cambridge University Press, Cambridge"},{"key":"9906_CR35","volume-title":"Complex networks","year":"2004","unstructured":"Ben-Naim E, Fraunenfelder H, Toroczkai Z (eds) (2004) Complex networks. Springer, Berlin"},{"key":"9906_CR36","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-7908-1854-3","volume-title":"Fuzzy graphs and fuzzy hypergraphs","author":"JN Mordeson","year":"2000","unstructured":"Mordeson JN, Nair PS (2000) Fuzzy graphs and fuzzy hypergraphs. Physica-Verlag, Heidelberg"},{"key":"9906_CR37","volume-title":"Fuzzy sets and fuzzy logic\u2014theory and applications","author":"GJ Klir","year":"1995","unstructured":"Klir GJ, Yuan B (1995) Fuzzy sets and fuzzy logic\u2014theory and applications. Prentice-Hall, Upper Saddle River"},{"key":"9906_CR38","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-8819-5","volume-title":"Weighted network analysis\u2014applications in genomics and systems biology","author":"S Horvath","year":"2011","unstructured":"Horvath S (2011) Weighted network analysis\u2014applications in genomics and systems biology. Springer, New York"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9906-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-016-9906-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9906-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-016-9906-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T01:37:04Z","timestamp":1744076224000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-016-9906-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3]]},"references-count":38,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,3]]}},"alternative-id":["9906"],"URL":"https:\/\/doi.org\/10.1007\/s10822-016-9906-3","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3]]},"assertion":[{"value":"28 January 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 March 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 March 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}