Redefining cheminformatics with intuitive collaborative mobile apps

Molecular Informatics

Volumn 31, Issue 8, 2012, Pages 569-584

  Clark, Alex M ^a   Ekins, Sean ^b   Williams, Antony J ^c  

^a Molecular Materials Informatics   (Canada)

^b Collaborations in Chemistry ^*  (United States)

^c ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

Author keywords

Apps; Chemistry; ChemSpider; Cloud Computing; Collaboration; Mobile Chemistry; Mobile Reagents; Web Services

Indexed keywords

CHEMINFORMATICS; CHEMSPIDER; CLOUD-COMPUTING; COLLABORATION; MOBILE APP; MOBILE CHEMISTRY; MOBILE REAGENT; SMART PHONES; TABLET COMPUTER; WEBS SERVICES;

WEB SERVICES;

ARTICLE; BIOCHEMISTRY; CHEMICAL REACTION; COMMUNICATION SOFTWARE; ELECTRONIC DATA INTERCHANGE; INTERNET; MEDICAL INFORMATICS; MOBILE PHONE; PHARMACEUTICS; PRIORITY JOURNAL; PRODUCTIVITY; WORKFLOW;

EID: 84865262647     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201200010     Document Type: Article

References (84)

1. S. Ekins, R. R. Gupta, E. Gifford, B. A. Bunin, C. L. Waller, Pharm. Res. 2010, 27, 2035-2039.
2. R. D. Cramer, D. E. Patterson, J. D. Bunce, J. Am. Chem. Soc. 1988, 110, 5959-5967.
3. G. Schneider, H.-J. Bohm, Drug Discov. Today 2002, 7, 64-70.
4. J. S. Mason, A. C. Good, E. J. Martin, Curr. Pharm. Design 2001, 7, 567-597.
5. P. W. Sprague, Perspect. Drug Discov. Design 1993, 3, 1-20.
6. D. Barnum, J. Greene, A. Smellie, P. Sprague, J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
7. M. E. Elyashberg, K. A. Blinov, Y. Smurnyy, T. Churanova, A. J. Williams, Magn. Resonance Chem. 2010, 48, 219-229.
8. Y. D. Smurnyy, K. A. Blinov, T. Churanova, M. E. Elyashberg, A. J. Williams, J. Chem. Inf. Model. 2008, 48, 128-134.
9. A. Yerin, A. J. Williams, Molecules (Basel, Switzerland) 1999, 4, 255-263.
10. Y. C. Martin, J. Med. Chem. 1992, 35, 2145-2154.
11. M. Hahn, J. Chem. Inf. Comput. Sci. 1995, 37, 80-86.
12. P. Willett, J. M. Barnard, G. M. Downs, J. Chem. Inf. Comp. Sci. 1998, 38, 983-996.
13. D. Kaiser, B. Zdrazil, G. F. Ecker, J. Comput. Aided Mol. Des. 2005, 19, 687-692.
14. D. Tapscott, A. J. Williams, Wikinomics: How Mass Collaboration Changes Everything, Portfolio, New York, 2006.
15. A. Bingham, S. Ekins, Drug Discov. Today 2009, 14, 1079-1081.
16. S. Ekins, A. J. Williams, Pharm. Res. 2010, 27, 393-395.
17. S. Ekins, A. J. Williams, The Future of Computational Models for Predicting Human Toxicities, ALTEX Proceedings, 1/12, Proceedings of WC8, 2012; http://www.altex.ch/resources/559554-EKinsandWilliams2.pdf.
18. Collaborative Computational Technologies for Biomedical Research (Eds:, S. Ekins, M. A. Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ, 2011.
19. S. Ekins, M. Hohman, B. A. Bunin, Collaborative Computational Technologies for Biomedical Research, Vol. 335-361 (Eds:, S. Ekins, M. A. Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ, 2011, pp. 335-362.
20. C. L. Waller, R. V. Duravasula, N. Lynch, Collaborative Computational Technologies for Biomedical Research, Vol. 335-361 (Eds:, S. Ekins, M. A. Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ, 2010, pp. 3-18.
21. S. Ekins, A. J. Williams, M. A. Z. Hupcey, Collaborative Computational Technologies for Biomedical Research, Vol. 335-361 (Eds:, S. Ekins, M. A.Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ, 2011, pp. 201-208.
22. E. L. Willighagen, J. Alvarsson, A. Andersson, M. Eklund, S. Lampa, M. Lapins, O. Spjuth, J. Wikberg, J. Biomed. Semantics 2011, 2 (Suppl 1), S1-S 6.
23. R. Guha, O. Spjuth, E. L. Willighagen, Collaborative Computational Technologies for Biomedical Research, Vol. 335-361 (Eds:, S. Ekins, M. A. Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ 2011, pp. 399-422.
24. O. Spjuth, E. L. Willighagen, R. Guha, M. Eklund, J. E. Wikberg, J. Cheminf. 2010, 2, 5.
25. O. Spjuth, T. Helmus, E. L. Willighagen, S. Kuhn, M. Eklund, J. Wagener, P. Murray-Rust, C. Steinbeck, J. E. Wikberg, BMC Bioinformatics 2007, 8, 59.
26. C. Steinbeck, C. Hoppe, S. Kuhn, M. Floris, R. Guha, E. L. Willighagen, Curr. Pharm. Design 2006, 12, 2111-2120.
27. B. Pratt, Collaborative Computational Technologies for Biomedical Research, Vol. 335-361 (Eds:, S. Ekins, M. A.Z. Hupcey, A. J. Williams,), Wiley, Hoboken, NJ, 2010, pp. 209-220.
28. B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. Gutlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky, S. Chawla, I. Ghosh, S. Ray, H. Patel, S. Escher, J. Cheminf. 2010, 2, 7.
29. R. R. Gupta, E. M. Gifford, T. Liston, C. L. Waller, B. Bunin, S. Ekins, Drug Metab. Dispos. 2010, 38, 2083-2090.
30. L. Carlsson, O. Spjuth, S. Adams, R. C. Glen, S. Boyer, BMC Bioinformatics 2010, 11, 362.
31. V. J. Sykora, D. E. Leahy, J. Chem. Inf. Model. 2008, 48, 1931-1942.
32. D. Lagorce, O. Sperandio, H. Galons, M. A. Miteva, B. O. Villoutreix, BMC Bioinformatics. 2008, 9, 396.
33. J. L. Melville, J. D. Hirst, J. Chem. Inf. Model. 2007, 47, 626-634.
34. I. Sushko, S. Novotarskyi, R. Korner, A. K. Pandey, M. Rupp, W. Teetz, S. Brandmaier, A. Abdelaziz, V. V. Prokopenko, V. Y. Tanchuk, R. Todeschini, A. Varnek, G. Marcou, P. Ertl, V. Potemkin, M. Grishina, J. Gasteiger, C. Schwab, Baskin, II, V. A. Palyulin, E. V. Radchenko, W. J. Welsh, V. Kholodovych, D. Chekmarev, A. Cherkasov, J. Aires-de-Sousa, Q. Y. Zhang, A. Bender, F. Nigsch, L. Patiny, A. J. Williams, V. Tkachenko, I. V. Tetko, J. Comp. Aided Mol. Des. 2011, 25, 533-554.
35. T. Walker, C. M. Grulke, D. Pozefsky, A. Tropsha, Bioinformatics (Oxford, England) 2010, 26, 3000-3001.
36. W. L. DeLano, The PyMOL Molecular Graphics System, 2002.
37. N. M. OâBoyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch, G. R. Hutchison, J. Cheminf. 2001, 3, 33.
38. G. Sandeep, K. P. Nagasree, M. Hanisha, M. M. Kumar, BMC Research Notes 2011, 4, 445.
39. A. P. Norgan, P. K. Coffman, J. P. Kocher, D. J. Katzmann, C. P. Sosa, J. Cheminf. 2011, 3, 12.
40. Evaluating the Productivity Impact of Mobile Devices, Nucleus Research, Boston, MA, 2011, Dec 15; WWW: http://nucleusresearch.com/research/notes-and- reports/evaluating-the-productivity-impact-of-mobile-devices/.
41. A. J. Williams, "Mobile Chemistry-Chemistry in Your Hands and in Your Face", Chemistry World, 2010 May.
42. A. J. Williams, S. Ekins, A. M. Clark, J. J. Jack, R. L. Apodaca, Drug Discov. Today 2011, 16, 928-939.
43. MIME Media Types, ICANN, Marina del Rey, CA, 2011, Dec 15; WWW: www.iana.org/assignments/media-types.
44. CTfile formats, Accelrys, San Diego, CA, 2011, Dec 15; WWW: http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee. php.
45. Dropbox, Dropbox, San Francisco, CA, 2011, Dec 15; WWW: http://www.dropbox.com.
46. SketchEl, Molecular Materials Informatics, Montréal, QC, 2011, Dec 15; WWW: http://molmatinf.com/fmtsketchel.html)
47. PDB file format, RCSB, Piscataway, NJ, 2011, Dec 15; WWW: http://www.wwpdb.org/docs.html.
48. Third party app development, Molecular Materials Informatics, Montréal, QC, 2011, Dec 15; WWW: http://molmatinf.com/mmdslib.html.
49. A. M. Clark, J. Chem. Inf. Model. 2011, 52, 3149-3157.
50. D. Weininger, J. Chem. Inf. Comput. Sci. 1988, 28, 31.
51. XML datasheet, Molecular Materials Informatics, Montréal, QC, 2011, Dec 15; WWW: http://molmatinf.com/fmtdatasheet.html.
52. P. Murray-Rust, H. S. Rzepa, J. Chem. Inf. Comput. Sci. 2003, 43, 757-772.
53. P. Murray-Rust, H. S. Rzepa, J. Chem. Inf. Model. 1999, 39, 928-942.
54. CDX File Format, Perkin-Elmer, Cambridge, MA, 2011, Dec 15; WWW: http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx.
55. Eidogen-Sertanty, Eidogen-Sertanty, Oceanside, CA, 2011, Dec 15; WWW: http://eidogen-sertanty.com.
56. Introduction to MolSync, Molecular Materials Informatics, Montréal, QC, 2011, Dec 15; WWW: http://molmatinf.com/intromolsync.html.
57. Protein Data Bank, RCSB, Piscataway, NJ, 2011, Dec 15; WWW: http://www.rcsb.org/pdb.
58. WebServices protocol, Molecular Materials Informatics, Montréal, QC, 2011, Dec 15; WWW: http://molmatinf.com/websvcproto.html.
59. Y. Wang, E. Bolton, S. Dracheva, K. Karapetyan, B. A. Shoemaker, T. O. Suzek, J. Wang, J. Xiao, J. Zhang, S. H. Bryant, Nucleic Acids Res. 2010, 38, D 255-266.
60. PubChem, NCBI, Bethesda, MD, 2011, Dec 15; WWW: http://pubchem.ncbi.nlm. nih.gov.
61. K. Degtyarenko, P. de Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcantara, M. Darsow, M. Guedj, M. Ashburner, Nucleic Acids Res. 2008, 36, D 344-350.
62. Open Melting points, Useful Chemistry, Philadelphia, PA, 2011, Dec 15; WWW: http://usefulchem.blogspot.com/2011/06/open-melting-points-on-iphone-via- mmds.html.
63. A. M. Clark, J. Cheminf. 2010, 2, 8.
64. A. J. Williams, Unreported results, manuscript in preparation, 2011.
65. V. Guagnano, P. Furet, C. Spanka, V. Bordas, M. Le Douget, C. Stamm, J. Brueggen, M. R. Jensen, C. Schnell, H. Schmid, M. Wartmann, J. Berghausen, P. Drueckes, A. Zimmerlin, D. Bussiere, J. Murray, D. Graus Porta, J. Med. Chem. 2011, 54, 7066-7083.
66. D. S. Weinstein, H. Gong, A. M. Doweyko, M. Cunningham, S. Habte, J. H. Wang, D. A. Holloway, C. Burke, L. Gao, V. Guarino, J. Carman, J. E. Somerville, D. Shuster, L. Salter-Cid, J. H. Dodd, S. G. Nadler, J. C. Barrish, J. Med. Chem. 2011, 54, 7318-7333.
67. A. K. Ganguly, S. S. Alluri, D. Caroccia, D. Biswas, C. H. Wang, E. Kang, Y. Zhang, A. T. McPhail, S. S. Carroll, C. Burlein, V. Munshi, P. Orth, C. Strickland, J. Med. Chem. 2011, 54, 7176-7183.
68. B. F. Jensen, C. Vind, S. B. Padkjaer, P. B. Brockhoff, H. H. Refsgaard, J. Med. Chem. 2007, 50, 501-511.
69. D. Fourches, E. Muratov, A. Tropsha, J. Chem. Inf. Model. 2010, 50, 1189-1204.
70. Office Open XML, Ecma International, Geneva, Switzerland, 2011, Dec 15; WWW: http://www.ecma-international.org/publications/standards/Ecma-376.htm.
71. Mobile Molecular DataSheet, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple.com/ca/app/mobile-molecular-datasheet/id383661863.
72. MolSync, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/ca/app/molsync/id461044999.
73. SAR Table, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/au/app/sar-table/id477451419.
74. Reaction101, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple.com/us/app/reaction101/id423115765.
75. Yield101, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/hk/app/yield101/id433416999.
76. MolPrime, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/us/app/molprime/id437087077.
77. Green Solvents, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple.com/us/app/green-solvents/id446670983.
78. American Chemical Society Green Chemistry Institute, American Chemical Society, Washington, DC, 2011, Dec 15; WWW: http://www.epa.gov/greenchemistry/ pubs/gcinstitute.html.
79. ChemSpider Mobile, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple.com/us/app/chemspider/id458878661.
80. Mobile Reagents, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple.com/us/app/mobilereagents/id395953310.
81. iProtein, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/us/app/iprotein/id380060128.
82. iKinase, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/us/app/ikinase/id348603129.
83. Kinase KnowledgeBase, Eidogen-Sertanty, Oceanside, CA, 2011, Dec 15; WWW: Available from: http://www.eidogen-sertanty.com/products-kinasekb.html.
84. Molecules, Apple, Cupertino, CA, 2011, Dec 15; WWW: http://itunes.apple. com/us/app/molecules/id284943090.