Sharing chemical relationships does not reveal structures

Journal of Chemical Information and Modeling

Volumn 54, Issue 1, 2014, Pages 37-48

  Matlock, Matthew ^a   Swamidass, S Joshua ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SHARING; ENCODING (SYMBOLS); INFORMATION DISSEMINATION; LIBRARIES; MOLECULES; PREDICTIVE ANALYTICS; SCAFFOLDS; SIGNAL ENCODING; TREES (MATHEMATICS);

CHEMICAL INFORMATION; CHEMICAL RELATIONSHIPS; COLLABORATIVE ANALYSIS; ECONOMIC OPTIMIZATION; SCREENING TECHNOLOGY; SMALL-MOLECULE LIBRARY; STRUCTURAL DESCRIPTORS; USEFUL CHEMICALS;

CHEMICAL ANALYSIS;

BIOLOGY; CHEMICAL DATABASE; CHEMICAL MODEL; CHEMICAL STRUCTURE; COMPUTER SECURITY; COOPERATION; INFORMATION DISSEMINATION; INFORMATION SCIENCE;

COMPUTATIONAL BIOLOGY; COMPUTER SECURITY; COOPERATIVE BEHAVIOR; DATABASES, CHEMICAL; INFORMATION DISSEMINATION; INFORMATION THEORY; MODELS, CHEMICAL; MOLECULAR STRUCTURE;

EID: 84893359147     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400399a     Document Type: Article

References (47)

1. Posner, B. A.; Xi, H.; Mills, J. E. J. Enhanced HTS hit selection via a local hit rate analysis J. Chem. Inf. Comput. Sci. 2009, 49, 2202-2210
2. Brideau, C.; Gunter, B.; Pikounis, B.; Liaw, A. Improved statistical methods for hit selection in high-throughput screening J. Biomol. Screen. 2003, 8, 634-647
3. Varin, T.; Gubler, H.; Parker, C.; Zhang, J.; Raman, P.; Ertl, P.; Schuffenhauer, A. Compound set enrichment: A novel approach to analysis of primary HTS data J. Chem. Inf. Comput. Sci. 2010, 50, 277-279
4. Swamidass, S. J.; Calhoun, B. T.; Bittker, J. A.; Bodycombe, N. E.; Clemons, P. A. Enhancing the rate of scaffold discovery with diversity-oriented prioritization Bioinformatics 2011, 27, 2271-2278
5. Swamidass, S. J.; Calhoun, B. T.; Bittker, J. A.; Bodycombe, N. E.; Clemons, P. A. Utility-aware screening with clique-oriented prioritization J. Chem. Inf. Comput. Sci. 2011, 52, 29-37
6. Swamidass, S. J. Using economic optimization to design high-throughput screens Future Med. Chem. 2013, 5, 9-11
7. Makarenkov, V.; Kevorkov, D.; Zentilli, P.; Gagarin, A.; Malo, N.; Nadon, R. HTS-Corrector: Software for the statistical analysis and correction of experimental high-throughput screening data Bioinformatics 2006, 22, 1408
8. Makarenkov, V.; Zentilli, P.; Kevorkov, D.; Gagarin, A.; Malo, N.; Nadon, R. An efficient method for the detection and elimination of systematic error in high-throughput screening Bioinformatics 2007, 23, 1648
9. Seiler, K.; George, G.; Happ, M.; Bodycombe, N.; Carrinski, H.; Norton, S.; Brudz, S.; Sullivan, J.; Muhlich, J.; Serrano, M.; Ferraiolo, P.; Tolliday, N.; Schreiber, S.; Clemons, P. ChemBank: A small-molecule screening and cheminformatics resource database Nucleic Acids Res. 2008, 36, D351
10. Calhoun, B. T.; Browning, M. R.; Chen, B. R.; Bittker, J. A.; Swamidass, S. J. Automatically detecting workflows in pubchem J. Biomol. Screen. 2012, 17, 1071-1079
11. Browning, M. R.; Calhoun, B. T.; Swamidass, S. J. Managing missing measurements in small-molecule screens J. Comput.-Aided Mol. Des. 2013, 27, 469-478
12. Schuffenhauer, A.; Ertl, P.; Roggo, S.; Wetzel, S.; Koch, M.; Waldmann, H. The scaffold tree-visualization of the scaffold universe by hierarchical scaffold classification J. Chem. Inf. Comput. Sci. 2007, 47, 47-58
13. Dimova, D.; Wawer, M.; Wassermann, A. M.; Bajorath, J. Design of multitarget activity landscapes that capture hierarchical activity cliff distributions J. Chem. Inf. Comput. Sci. 2011, 51, 258-266
14. Wassermann, A. M.; Bajorath, J. Directed R-group combination graph: A methodology to uncover structure-activity relationship patterns in a series of analogues J. Med. Chem. 2012, 55, 1215-1226
15. Griffen, E.; Leach, A. G.; Robb, G. R.; Warner, D. J. Matched molecular pairs as a medicinal chemistry tool J. Med. Chem. 2011, 54, 7739-7750
16. Howells, J.; Gagliardi, D.; Malik, K. Sourcing knowledge: R&D outsourcing in U.K. pharmaceuticals Int. J. Technol. Manage. 2012, 59, 139-161
17. Fox, S.; Farr-Jones, S.; Sopchak, L.; Boggs, A.; Nicely, H.; Khoury, R.; Biros, M. High-throughput screening: Update on practices and success J. Biomol. Screen. 2006, 11, 864
18. McGee, J. Outsourcing and contract services J. Biomol. Screen. 2012, 17, 1379-1381
19. Swamidass, S. J. Mining small-molecule screens to repurpose drugs Briefings Bioinf. 2011, 12, 327-335
20. Baell, J.; Holloway, G. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays J. Med. Chem. 2010, 53, 2719-2740
21. Bradley, D. Share and share alike Nat. Rev. Drug Discovery 2005, 4, 180-180
22. Masek, B. B.; Shen, L.; Smith, K. M.; Pearlman, R. S. Sharing chemical information without sharing chemical structure J. Chem. Inf. Comput. Sci. 2008, 48, 256-261
23. Balaban, A. Can topological indices transmit information on properties but not on structures? J. Comput.-Aided Mol. Des. 2005, 19, 651-660
24. Bologa, C.; Allu, T.; Olah, M.; Kappler, M.; Oprea, T. Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures J. Comput.-Aided Mol. Des. 2005, 19, 625-635
25. Clement, O.; Güner, O. Possibilities for transfer of relevant data without revealing structural information J. Comput.-Aided Mol. Des. 2005, 19, 731-738
26. Filimonov, D.; Poroikov, V. Why relevant chemical information cannot be exchanged without disclosing structures J. Comput.-Aided Mol. Des. 2005, 19, 705-713
27. Kaiser, D.; Zdrazil, B.; Ecker, G. Similarity-based descriptors (SIBAR)-A tool for safe exchange of chemical information? J. Comput.-Aided Mol. Des. 2005, 19, 687-692
28. Trepalin, S.; Osadchiy, N. The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets J. Comput.-Aided Mol. Des. 2005, 19, 715-729
29. Tetko, I. V.; Abagyan, R.; Oprea, T. I. Surrogate data-A secure way to share corporate data J. Comput.-Aided Mol. Des. 2005, 19, 749-764
30. Karr, A. F.; Feng, J.; Lin, X.; Sanil, A. P.; Young, S. S.; Reiter, J. P. Secure analysis of distributed chemical databases without data integration J. Comput.-Aided Mol. Des. 2005, 19, 739-747
31. Faulon, J.-L.; Brown, W. M.; Martin, S. Reverse engineering chemical structures from molecular descriptors: How many solutions? J. Comput.-Aided Mol. Des. 2005, 19, 637-650
32. Bzip2, version 1.0.6. http://www.bzip.org (accessed July 7, 2013).
33. James, C. A.; Weininger, D.; Delany, J. (Daylight Chemical Information Systems) Daylight Theory Manual, 2005. http://www.daylight.com/dayhtml/doc/ theory/ (accessed July 7, 2013).
34. Weininger, D. Method and apparatus for designing molecules with desired properties by evolving successive populations. U.S. Patent 5,434,796, 1995.
35. Faulon, J.-L.; Churchwell, C. J.; Visco, D. P. The signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences J. Chem. Inf. Comput. Sci. 2003, 43, 721-734
36. Hohman, M.; Gregory, K.; Chibale, K.; Smith, P.; Ekins, S.; Bunin, B. Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery Drug Discovery Today 2009, 14, 261-270
37. Gupta, R.; Gifford, E.; Liston, T.; Waller, C.; Hohman, M.; Bunin, B.; Ekins, S. Using open-source computational tools for predicting human metabolic stability and additional ADME/TOX properties Drug Metab. Dispos. 2010, 11, 2083-2090
38. Allison, M. NCATS launches drug repurposing program Nat. Biotechnol. 2012, 30, 571-572
39. Bolton, E.; Wang, Y.; Thiessen, P.; Bryant, S. PubChem: Integrated platform of small molecules and biological activities Annu. Rep. Comput. Chem. 2008, 4, 217-241
40. Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39, 2887-2893
41. McKay, B. D. Nauty User's Guide, version 2.4; Computer Science Dept., Australian National University: Acton, Australia, 2007.
42. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Cheminf. 2011, 3 Article 33 http://www.jcheminf.com/content/3/1/33
43. O'Boyle, N.; Morley, C.; Hutchison, G. Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2 Article 5 http://journal.chemistrycentral.com/content/2/1/5
44. Liu, W.-H.; Sherman, A. H. Comparative analysis of the Cuthill-McKee and the reverse Cuthill-McKee ordering algorithms for sparse matrices SIAM J. Num. Anal. 1976, 13, 198-213
45. Sporzynski, S. Implementation and use of high-performance parallel skyline matrix subroutines on the IBM vector facility Comput. Syst. Eng. 1991, 2, 203-215
46. Silva, M. Sparse matrix storage revisited. In Proceedings of the 2nd Conference on Computing Frontiers; Association for Computing Machinery: New York, NY, 2005; pp 230-235.
47. Itti, L.; Baldi, P. Bayesian surprise attracts human attention Adv. Neural Inf. Process. Syst. 2006, 18, 547