Abstract
For over a decade, cheminformatics has contributed to a wide array of scientific tasks from analytical chemistry and biochemistry to pharmacology and drug discovery; and although its contributions to decision making are recognized, the challenge is how it would contribute to faster development of novel, better products. Here we address the future of cheminformatics with primary focus on innovation. Cheminformatics developers often need to choose between “mainstream” (i.e., accepted, expected) and novel, leading-edge tools, with an increasing trend for open science. Possible futures for cheminformatics include the worst case scenario (lack of funding, no creative usage), as well as the best case scenario (complete integration, from systems biology to virtual physiology). As “-omics” technologies advance, and computer hardware improves, compounds will no longer be profiled at the molecular level, but also in terms of genetic and clinical effects. Among potentially novel tools, we anticipate machine learning models based on free text processing, an increased performance in environmental cheminformatics, significant decision-making support, as well as the emergence of robot scientists conducting automated drug discovery research. Furthermore, cheminformatics is anticipated to expand the frontiers of knowledge and evolve in an open-ended, extensible manner, allowing us to explore multiple research scenarios in order to avoid epistemological “local information minimum trap”.
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References
Retrieved from Wikipedia, http://en.wikipedia.org/wiki/Athanasius_Kircher. Accessed 8 Dec 2011
Retrieved from ECHO (European Cultural Heritage Online), http://echo.mpiwg-berlin.mpg.de/ECHOdocuViewfull?pn=42&ws=2.5&cont=0..6&start=41&viewMode=images&mode=imagepath&url=/mpiwg/online/permanent/library/ZYCRR6CN/pageimg. Accessed 8 Dec 2011
Oprea TI (2002) Molecules 7:51
Retrieved from “Who first said “It is difficult to make predictions, especially about the future” (or one of its many variants)?” http://www.larry.denenberg.com/predictions.html. Accessed 8 Dec 2011
Gasteiger J (ed) (2003) Handbook of Chemoinform. Wiley-VCH, Weinheim, 1871 p
Oprea TI, Tropsha A, Faulon JL, Rintoul MD (2007) Nat Chem Biol 3:447
Oprea TI, May EE, Leitão A, Tropsha A (2011) Computational systems chemical biology. In: Bajorath J (ed) Chemoinformatics and computational chemical biology, methods in molecular biology, vol 672. Springer, Berlin, pp 459–488
Oprea TI, Tropsha A (2006) Drug Discov Today Technol 3:357
Mestres J, Seifert SA, Oprea TI (2011) Clin Pharmacol Ther 90:662
Abernethy DR, Bai JPF, Burkhart K, Xie HG, Zhichkin P (2011) Clin Pharmacol Ther 90:645
Fenner JW, Brook B, Clapworthy G, Coveney PV, Feipel V, Gregersen H, Hose DR, Kohl P, Lawford P, McCormack KM, Pinney D, Thomas SR, Van Sint Jan S, Waters S, Viceconti M (2008) Philos Trans A Math Phys Eng Sci 366:2979
Schuster SC (2008) Nat Methods 5:16
Wang L, Khankhanian P, Baranzini SE, Mousavi P (2011) BMC Bioinform 12:380
Oprea TI, Nielsen SK, Ursu O, Yang JJ, Taboureau O, Mathias SL, Kouskoumvekaki I, Sklar LA, Bologa CG (2011) Mol Inf 30:100
Abeyruwan S, Chung C, Datar N, Gayanilo F, Koleti A, Lemmon V, Mader C, Ogihara M, Puram D, Sakurai K, Smith R, Vempati U, Venkatapuram S, Visser U, Schürer S (2010) Semantic web challenge 9th international semantic web conference ISWC 1–12, http://www.cs.vu.nl/~pmika/swc/submissions/swc2010_submission_20.pdf
Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ (2010) BMC Bioinform 11:255
Berners-Lee T, Hendler J, Lassila O (2001) Sci Am 284:34
Rosenbaum S (2011) Curation nation. McGraw-Hill, New York, 304 p
Retrieved from OpenPHACTS, http://www.openphacts.org. Accessed 8 Dec 2011
Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtalen HE, Schramm KW, Shen H, Variainen T, Kiviranta H, Taboureau O, Brunak S, Main KM (2010) Int J Androl 33:270
Ruzzin J, Petersen R, Meugnier E, Madsen L, Lock EJ, Lillefosse H, Ma T, Pesenti S, Sonne SB, Marstrand TT, Malde MK, Du ZY, Chavey C, Fajas L, Lundebye AK, Brand CL, Vidal H, Kristiansen K, Frøyland L (2010) Environ Health Perspect 118:465
Kovakic P, Somanathan R (2009) Rev Environ Contam Toxicol 201:41
Shardlow CE, Generaux GT, MacLaunchlin CC, Pons N, Skordos KW, Bloomer JC (2011) Drug Metab Dispos 39:2076
Wigle DT, Arbuckle TE, Walker M, Wade MG, Liu S, Krewski D (2007) J Toxicol Environ Health 10:3
Hardy B, Douglas N, Helma C, Rautenberg M, Jeliazkova N, Jeliazkov V, Nikolova I, Benigni R, Tcheremenskaia O, Kramer S, Girschick T, Buchwald F, Wicker J, Karwath A, Gütlein M, Maunz A, Sarimveis H, Melagraki G, Afantitis A, Sopasakis P, Gallagher D, Poroikov V, Filimonov D, Zakharov A, Lagunin A, Gloriozova T, Novikov S, Skvortsova N, Druzhilovsky D, Chawla S, Ghosh I, Ray S, Patel H, Escher S (2010) J Cheminform 2:7
Retrieved from the REACH website, http://ec.europa.eu/enterprise/sectors/chemicals/reach/index_en.htm. Accessed 8 Dec 2011
King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A (2009) Science 324:85
Retrieved from https://www.23andme.com. Accessed 8 Dec 2011
Oprea TI, Bauman JE, Bologa CG, Buranda T, Chigaev A, Edwards BS, Jarvik JW, Gresham HD, Haynes MK, Hjelle B, Hromas R, Hudson L, Mackenzie DA, Muller CY, Reed JC, Simons PC, Smagley Y, Strouse J, Surviladze Z, Thompson T, Ursu O, Waller A, Wandinger-Ness A, Winter SS, Wu Y, Young SM, Larson RS, Willman CL, Sklar LA (2011) Drug Discov Today: Therap Strategies, doi:10.1016/j.ddstr.2011.10.002
Gibson WM (1971) Can Fam Physician 17:29
Auffray C, Chen Z, Hood L (2009) Genome Med 1:2
Horgan J (1997) The end of science: facing the limits of science in the twilight of the scientific age. Broadway Books, New York, 322 p
Taleb NN (2007) The black swan. Random House, New York, 400 p
Popper KR (1935) The logic of scientific discovery. Routledge Classics (reprinted), New York, 510 p
Retrieved from http://hsc.unm.edu/som/biocomputing/carlsbad. Accessed 8 Dec 2011
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Genome Res 13:2498
Oprea TI, Bologa CG, Boyer S, Curpan RF, Glen RC, Hopkins AL, Lipinski CA, Marshall GR, Martin YC, Ostopovici-Halip L, Rishton G, Ursu O, Vaz RJ, Waller CL, Waldmann H, Sklar LA (2009) Nat Chem Biol 5:441
Acknowledgments
This work was supported in part by NIH grants GM-095952, MH-084690, and CA-118100 (TIO, CGB), and by the Villum Foundation CDSB (TIO). This work was supported by the Innovative Medicines Initiative Joint Undertaking (OpenPHACTS).
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Oprea, T.I., Taboureau, O. & Bologa, C.G. Of possible cheminformatics futures. J Comput Aided Mol Des 26, 107–112 (2012). https://doi.org/10.1007/s10822-011-9535-9
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DOI: https://doi.org/10.1007/s10822-011-9535-9