Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 5, 2011, Pages 427-441

  Robson, Barry ^a,b   Li, Jin ^c   Dettinger, Richard ^d   Peters, Amanda ^e   Boyer, Stephen K ^f  

^a Saint Matthews University School of Medicine   (Cayman Islands)

^b UNIVERSITY OF WISCONSIN STOUT   (United States)

^c ASTRAZENECA   (United Kingdom)

^d Prentice   (United States)

^e HARVARD UNIVERSITY   (United States)

^f Collabra Inc ^*  (United States)

Author keywords

Drug discovery; Ligand design; Patent analytics; Regular expression; Similarity

Indexed keywords

CLASSIFICATION (OF INFORMATION); GENES; PATENTS AND INVENTIONS; PATTERN MATCHING;

BLUE GENE; CHEMICAL SIMILARITY; DATA BASE; DRUG DISCOVERY; LIGAND DESIGN; MUTUAL INFORMATIONS; PATENT ANALYTIC; PATENT DATUM; REGULAR EXPRESSIONS; SIMILARITY;

DATA MINING;

CARBENOXOLONE; LIGAND; THIOKETONE;

ALGORITHM; ARTICLE; COMPUTER AIDED DESIGN; COMPUTER SYSTEM; CONTROLLED STUDY; DATA MINING; DRUG DETERMINATION; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; EVOLUTION; INFORMATION PROCESSING; MOLECULAR DYNAMICS; NATURAL SELECTION; PATENT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN TARGETING; TAXONOMY; THEORY; WORKFLOW;

EID: 80051706196     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9429-x     Document Type: Article

References (54)

1. Adams RS (2006) Information sources in patents. Walter de Gruyter: Amsterdam, The Netherlands
2. Lynch MF, Barnard JM, Welford SM (1981) Computer Storage and retrieval of generic chemical structures in patents, 1. Introduction and general strategy. J Chem Inf Comp Sci 21(3): 148-150
3. Downs GM, Barnard JM (1998) Chemical patents and structural information: The Sheffield research in context. J Documentation 54(1):106-120
4. Oldach S, Stabinsk N (2009) The value of patent analytics, 2008. Intellectual property today. http://www.iptoday.com/articles/ 2008-6-oldach.asp. Accessed 20 Mar 2009
5. Feldman R, Sanger J (2006) The text mining handbook: advanced approaches in analyzing unstructured data. Cambridge University Press, Cambridge
6. Berks AH (2001) Current state of the art of Markush topological search systems. World Patent Inf 23(1):5-13
7. Li J, Robson B (2000) Bioinformatics and computational chemistry in molecular design. Recent advances and their application. In Peptide and Protein Drug Analysis, Marcel Dekker NY, 285-307
8. Paolini GV, Shapland HBR, van Hoorn WP, Mason JS, Hopkins AL (2006) Global mapping pharmaceutical space. Nat Biotechnol 24(7):805-815
9. Chen YP, Chen F (2008) Identifying targets for drug discovery using bioinformatics. Expert Opin Ther Targets 12(4):383-389 (Pubitemid 351546366)
10. Digital Chemistry (2009) Digital chemistry. http://www.digital chemistry.co.uk/prod-torus-patent.htm. Accessed 20 Jul 2009
11. Reel Two, Reel Two web site (2007) http://www.reeltwo.com/. Accessed 20 Jul 2009
12. Tripos Inc (2008) http://www.tripos.com/data/support/mol2.pdf. Accessed 5 Apr 09
13. Symyx, Symyx Web Page (2009) http://www.symyx.com. Accessed 10 Nov 2009
14. Grant JA, Haigh JA, Pickup BT, Nicholls A, Sayle RA (2006) Lingos, finite state machines, and fast similarity searching. J Chem Inf Model 46(5):1912-1918 (Pubitemid 44625962)
15. Haque IS, Pande VS, Walters WP (2010) SIML: A fast SIMD algorithm for calculating LINGO chemical similarities on GPUs. J Chem Inf Model 50:560-564
16. Rhodes J, Boyer S, Kreulen J, Chen Y, Ordonez P (2007) Mining patents using molecular similarity search. pacific symposium on biocomputing, Maui, Hawaii, 3-7 January 2007 Ed. Altman et al. World Scientific Publishing; p 304-315, http://www.almaden.ibm.com/asr/projects/biw/publications/Rhodes.pdf
17. Chen Y, Spangler S, Kreulen J, Boyer SK (2009) SIMPLE: A strategic information mining platform for IP excellence. In: IEEE international conference on data mining workshops, Miami, Florida, 6 Dec 2009. p 270-275. http://domino.research.ibm.com/library/cyberdig.nsf/papers/ 95D73078344701C9852576350055DBF3/File/rj10450.pdf
18. Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comp Sci 28:31-36 (Pubitemid 18574254)
19. The Open Group, Regular Expressions (2009) The Single UNIX ̊ Specification, Version 2, 1997. Opengroup.org. http://www. opengroup.org/ onlinepubs/007908799/xbd/re.html. Accessed 1 Aug 2009
20. Wall L, The Perl Development Team (2006) Perl.org.http://perldoc.perl. org/perlre.html. Accessed 9/1/2009
21. Fisanick W (1990) The chemical abstracts service generic chemical (Markush) structure storage and retrieval capability. 1. Basic concepts. J Chem Inf Comp Sci 30(2):145-154
22. Barnard JM (1991) A comparison of different approaches to Markush structure handling. J Chem Inf Comp Sci 31(1):64-68
23. Barnard JM (1993) Substructure searching methods: old and new. J Chem Inf Comp Sci 33(4):532-538
24. Barnard JM, Downs GM (1997) Chemical fragment generation and clustering software. J Chem Inf Comp Sci 37(1):141-142
25. Downs GM, Barnard JM (1997) Techniques for generating descriptive fingerprints in combinatorial libraries. J Chem Inf Comp Sci 37(1):59-61 (Pubitemid 127601578)
26. Barnard JM, Downs GM (1992) Clustering of chemical structures on the basis of two-dimensional similarity measure. J Chem Inf Comp Sci 32(6):644-649
27. Brown RD, Martin YC (1996) Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J Chem Inf Comp Sci 36:572-584 (Pubitemid 126539358)
28. Robson B, Finn PW (1984) Rational design of conformationally flexible drugs. ATLA Journal. Alternatives to Laboratory Animals 11: 67-78
29. Ivanciuc O (2003) Canonical numbering and constitutional symmetry. In: Handbook of Chemoinformatics, Ed. J. Gasteiger, Wiley-VCH, pp 139-160
30. Daylight Chemical Systems, Inc (2009) http://www.daylight.com/. Accessed 10 Apr 2009
31. Dethlefsen W, Lynch MF, Gillet VJ, Downs GM, Holliday JD, Barnard JM (1991) Computer storage and retrieval of generic chemical structures in patents. 12. Principles of search operations involving parameter lists: matching-relations, user-defined match levels, and transition from the reduced graph search to the refined search. J Chem Inf Comp Sci 31(2):253-260
32. Robson B (1974) Analysis of the code relating sequence to conformation in globular proteins: theory and application of expected information. Biochem J 141:853-867
33. Robson B (2008) Clinical and pharmacogenomic data mining: 4. The FANO program and command set as an example of tools for biomedical discovery and evidence based medicine. J Proteome Res 7(9):3922-3947
34. Wikepedia (2010) http://en.wikipedia.org/wiki/IUPAC-nomenclature.Accessed 8/30/2010
35. Wikepedia (2010) Wikepedia. http://en.wikipedia.org/wiki/Blue-Gene. Accessed 8/3/09
36. Kramer A, Horn HW, Rice J (2003) Fast 3D molecular superposition and similarity search in databases of flexible molecules. J Comp Aided Mol Des 17(1):13-38 (Pubitemid 36939538)
37. IBM Corporation, Data Discovery and Query Builder's User's Guide (2006) IBM Corporation. http://publib.boulder.ibm.com/infocenter/systems/topic/ddqb/ v2r1ddqbusersguide.pdf. Accessed 7 Apr 2009
38. University of California San Francisco, http://zinc.docking.org/. Accessed 8 Aug 2009
39. RCSB Protein data Bank (2008) http://www.wwpdb.org/docs.html. Accessed 5 Apr 2009
40. Warner J (2004) Licorice root may keep mental skills sharp: compound derived from licorice root may fight effects of aging on brain. 2004, March. WebMD News. http://www.webmd.com/alzheimers/news/20040329/licorice-root-may- keep-mental-skillssharp.Accessed 5 Apr 2009
41. Livingstone DE, Walker BR (2003) Is 11beta-hydroxysteroid dehydrogenase type 1 a therapeutic target? Effects of carbenoxolone in lean and obese Zucker rats. J Pharmacol Exp Ther 305(1):167-172 (Pubitemid 36373847)
42. Wikepedia (2009) http://en.wikipedia.org/wiki/Zipf's-law. Accessed 6 Aug 2009
43. CAS, a division of the American Chemical Society. Support Page (2009) http://www.cas.org/support/scifi/index.html. Accessed 1 Jan 2010
44. CAS, a division of the American Chemical Society, Products page (2009) http://www.cas.org/products/sfacad/index.html. Accessed1 Jan 2010
45. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Su S, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comp Chem 14:1347-1363
46. Peters A, Lundberg M, Sosa CP, Lang T (2007) High throughput computing validation for drug discovery using the DOCK program on a massively parallel system. 1st annual MSCBB, Northwestern University, Evanston, IL, September 2007; available as Peters A, Lundberg M, Lang T, and Sosa, CP, 2008, RedPaper 4410 from IBM Corporation Poughkeepsie, NY
47. Balius TE, Mukherjee S (2008) Stony Brook University web site. http://www.ams.sunysb.edu/*tbalius/NamdandDockonNYBlue.pdf. Accessed 8 Aug 2009
48. Shivakumar D (2008) (updated 2009). University of California San Francisco, http://dock.compbio.ucsf.edu/DOCK-6/tutorials/amber-score/amber- score.htm. Accessed 12 Aug 2009
49. McWeeny R (1979) Coulson's Valence, 3rd edn. Oxford University Press, Oxford, UK see Ch. 6
50. Robson B, Curioni A, Mordasini T (2002) Studies in the assessment of folding quality for protein modeling and structure prediction. J Proteome Res (Am Chem Soc) 1(2):115-133 (Pubitemid 36050261)
51. Robson B, Vaithilingham A (2008) "Protein Folding Revisited" pp 161-202 in Progess in Molecular Biology and Translational Science, Vol 84: Molecular Biology of Protein Folding, Elsevier Press/Academic Press
52. Robson B, Douglas GM, Platt E (1982) A new algorithm for rapid calculation of conformational energies. Biochem Soc Trans 10:388-389
53. Robson B, Platt E (1986) Refined models for computer calculations in protein engineering. Calculation and testing of atomic potential functions compatible with more efficient calculations. 188: 259-281
54. Collura VP, Greaney PJ, Robson B (1994) A method for rapidly assessing and refining simple solvent treatments in molecular modeling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603. Protein Eng 7:221-233