Current Trends in Cheminformatics
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1 Current Trends in Cheminformatics Dr. Wendy A. Warr
2 Overview Literature analysis Hardware and infrastructure Web 2.0 The Semantic Web Text mining Combichem Evaluation of scientific methods Conclusions
3 Bibliometric Analysis Willett, P. A bibliometric analysis of the literature of chemoinformatics. Aslib Proc. 2008, 60(1),
4 Citation Analysis - Caveat Must cites Reviews and perspectives Bias toward older papers Etc.
5 Trend Toward Applications Willett, P. A bibliometric analysis of the Journal of Molecular Graphics and Modelling.. J. Mol. Graphics Modell. 2007, 26(3) (3),
6 Highly Cited 1. Koradi et al.. MOLMOL: a program for display and analysis of of macromolecular structures. J. Mol. Graphics Modell. 1996, 14, (3298 citations) 10. Dunker et al.. Intrinsically disordered protein. J. Mol. Graphics Modell. 2001, 19, (242) 11. Golbraikh,, A.; Tropsha,, A. Beware of q 2! J. Mol. Graphics Modell. 2002, 20, (172)
7 JCIM J. Chem. Inf. Comput. Sci. (JCICS) is now J. Chem. Inf. Model. (JCIM)
8 Most Cited JCICS-JCIM JCIM Paper Allen, F. H.; Davies, J. E.; Galloy,, J. J.; Johnson, O.; Kennard, O.; Macrae,, C. F.; Mitchell, E. M.; Mitchell, G. F.; Smith, J. M.; Watson, D. G. The development of versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 1991, 31,
9 Most Cited JCICS-JCIM JCIM since Fletcher, D. A.; McMeeking,, R. F.; Parkin,, D. The United Kingdom chemical database service. J. Chem. Inf. Comput. Sci. 1996, 36,, HIGHER 2. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 1998, 38,, HIGHER 3. Brown, R. D.; Martin, Y. C. Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 1996, 36,, (compare 2005 rank)
10 Most Cited JCICS-JCIM JCIM May 2008 versus July Oprea,, T. I.; Davis, A. M.; Teague, S. J.; Leeson,, P. D. Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Comput. Sci. 2001,, 41, HIGHER 5. Hann,, M. M.; Leach, A. R.; Harper, G. Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci. 2001, 41, HIGHER 6. Wessel,, M. D.; Jurs,, P. C.; Tolan,, J. W.; Muskal,, S. M. Prediction of human intestinal absorption of drug compounds from molecular structure. J. Chem. Inf. Comput. Sci. 1998, 38,, HIGHER
11 Most Cited JCICS-JCIM JCIM May 2008 versus July Brown, R. D.; Martin, Y. C. The information content of 2D and 3D structural descriptors relevant to ligand- receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37,, HIGHER 8. Platts,, J. A.; Butina,, D.; Abraham, M. H.; Hersey,, A. Estimation of Molecular Linear Free Energy Relation Descriptors Using a Group Contribution Approach. J. Chem. Inf. Comput. Sci. 1999; 39,, HIGHER 9. Irwin, J. J.; Shoichet,, B. K. ZINC - A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45,, NEW
12 Most Cited JCICS-JCIM JCIM May 2008 versus July Pearlman, R. S.; Smith, K. M. Metric Validation and the receptor-relevant relevant subspace concept. J. Chem. Inf. Comput. Sci. 1999, 39,, HIGHER 11. Wildman, S. A.; Crippen,, G. M. Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comput. Sci. 1999, 39, NEW 12. Kearsley,, S. K.; Sallamack,, S.; Fluder,, E. M.; Andose,, J. D.; Mosley, R. T.; Sheridan, R. P. Chemical similarity using physiochemical property descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, NEW 13. Hawkins, D. M. The problem of overfitting. J. Chem. Inf. Comput. Sci. 2004, 44,, NEW
13 Most Cited JCICS-JCIM JCIM May 2008 versus July Randic,, M.; Vracko,, M.; Nandy,, A.; Basak,, S. C. On 3-D D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inf. Comput. Sci. 2000, 40,, NEW 15. Katritzky,, A. R.; Maran,, U.; Lobanov,, V. S.; Karelson,, M. Structurally diverse quantitative structure-property relationship correlations of technologically relevant physical properties. J. Chem. Inf. Comput. Sci. 2000, 40,, NEW 16. Wang, R.; Fu, Y.; Lai, L. A new atom-additive additive method for calculating partition coefficients. J. Chem. Inf. Comput. Sci. 1997,, 37, NEW
14 Most Cited JCICS-JCIM JCIM May 2008 versus July Lewell,, X. Q.; Judd, D. B.; Watson, S. P.; Hann,, M. M. RECAP-retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci. 1998, 38,, NEW 18. Rusinko,, A., III; Farmen,, M. W.; Lambert, C. G.; Brown, P. L.; Young, S. S. Analysis of a large structure/biological activity data set using recursive partitioning. J. Chem. Inf. Comput. Sci. 1999, 39, NEW
15 Most Cited JCICS-JCIM JCIM May 2008 versus July Tong, W.; Lowis,, D. R.; Perkins, R.; Chen, Y.; Welsh, W. J.; Goddette,, D. W.; Heritage, T. W.; Sheehan, D. M. Evaluation of quantitative structure- activity relationship methods for large-scale prediction of chemicals binding to the estrogen receptor. J. Chem. Inf. Comput. Sci. 1998, 38,, NEW 20. Huuskonen,, J. Estimation of aqueous solubility for a diverse set of organic compounds based on molecular topology. J. Chem. Inf. Comput. Sci. 2000,, 40, NEW
16 Fearless Predictions Where a calculator on the Eniac is equipped with 18,000 vacuum tubes and weighs 30 tons, computers in the future may have only 1,000 vacuum tubes and perhaps weigh 1.5 tons. Popular Mechanics, March 1949
17 1984 VAX 11/750 Clock speed 6 MHz 2 Mb memory 134 Mb fixed disk Two 67 Mb exchangeable disk drives Shared peripherals 100,000 (1984 price)
18 1992 PC IBM-compatible, MS-DOS 2.1 or higher machine 640K memory a floppy drive (3.5-in. 1.44MB or 5.25 in. 1.2MB) hard disk with at least 6MB available EGA or Hercules display Bretherick's Reactive Chemical Hazards Database Version 1.00
19 Infrastructure 2008 Cyberinsfrastructure/e-science science Grid computing Web 2.0 The Semantic Web
20 A Mobile CAS Service
21 SciTegic Pipeline Pilot
22 Workflow and Pipelining Kepler Taverna SOMA Pipeline Pilot InforSense KNIME qsar-workflow1.php
23 Data Cartridges Symyx Direct Accelrys Accord Chemistry Cartridge Daylight DayCart ChemAxon JChem Cartridge CambridgeSoft Oracle Cartridge InfoChem IC Cartridge Tripos AUSPYX IDBS ChemXtra Dotmatics Pinpoint Digital Chemistry Torus Source: DeltaSoft Inc.
24 Social Software Instant messaging MSN Messenger, Yahoo Messenger, AOL Instant Messenger, Skype Text chat Internet Relay Chat Internet forums Blogs Wikis Wikipedia
25 Social Software Blog search engines Google blogsearch, Technorati Web feeds RSS Rich Site Summary/Really Simple Syndication Atom Podcasts Can be syndicated, subscribed to etc.
26 Social Software Social network services Facebook, MySpace, Flickr, YouTube LinkedIn, Ryze,, XING Social guides WikiTravel, TripAdvisor Social bookmarking Tagging, tag clouds, folksonomy Social citations CiteULike, Connotea, BibSonomy Virtual worlds
27 Most Popular Web Sites 1. Yahoo 2. Google 3. MSN 4. YouTube 5. Live 6. MySpace 7. Orkut 8. Facebook 9. Wikipedia 10. Hi5 English language sites, Alexa,, October 7, 2007
28 RSC Project Prospect
29 RSC Project Prospect
30 InChI Goal Provide a unique string representing a chemical substance of known structure independent of specific depiction derived from conventional connection table freely available extensible
31 InChI Example L-ascorbic acid InChI=1/C6H8O6/c7 =1/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-10H,1H2/t2-,5+/m0/s1,5+/m0/s1
32 InChIKey InChI=1/C17H19NO3/c1 =1/C17H19NO3/c (20)16(17) (19)4-2-9(14(15)17)8-11(10)18/h2-5,10 5,10-11,13,16,19-20H,6-8H2,1H3/t10-,11-,13-,16-,17-/m0/s1 InChIKey = BQJCRHHNABKAKU-XKUOQXLYBY
33 Words, words, words The Lord s s Prayer uses 56 words The Ten Commandments, 297 words The American Declaration of Independence, 300 words The EEC Directive on the import of caramel and caramel products uses 26,911 words
34 Information Extraction Technologies in Chemistry ch07/slides/hofmann.pdf Martin Hofmann-Apitius
35 Chemical Named Entity Recognition (NER) TEMIS InforSense SciTegic Open Source Chemical Analysis Routines (OSCAR) IBM Chemical Annotator
36 Name to Structure CambridgeSoft Name=Struct ACD/Labs Name to Structure OpenEye Lexichem InfoChem IC ICN2S
37 Structures from Images Kekulé (JCICS 1992) CLiDE (Peter Johnson Key Module) OSRA (NIH Cactus) chemocr (Fraunhofer/InfoChem)
38 O NH 2 N O N O N O O O O O N O O O Molecular Diversity Br OH N O N N O O O O O O O O P O NH O O N R 1 O
39 How Big is Readily Accessible Chemistry Space? R1 N diamine N R2 = 2.0x X 4145 X = 2.0x10 R1 = R2 = acylating reagents, cleanly displaceable halides, amines (to ureas via ClC(= (=O)Cl),), reductive amination substrates Counts refer to Available Chemicals Directory (ACD) Source: Tripos (as of 1995?) 2.0x10 13 = 40 million pharma decks = 1,000,000 x compounds ever reported (Chemical Abstracts) = 60,000 years of rate of one million per day
40 Library Design Random screening is too expensive Its hit rate is low False positives may be a problem HTS consumes expensive compounds There are too many possible compounds How to choose those most likely to be hits?
41 Selection possible drugs likely drugs known compounds commercially available in corporate databases in drug databases commercial drugs profitable drugs Source: David Weininger
42 Instead of blockbusters and me-toos Translational research Pharmacogenomics Biomarkers Personalized medicine
43 Generic Structure R 3 Cl OH (CH 2 ) n R 1 R 2 substituent variation R 1 is methyl or ethyl homology variation R 2 is alkyl position variation R 3 is amino frequency variation n is 1-31 Source: John Barnard
44 Compound characterisation Barreiro,, G.; Guimaraes,, C. R. W.; Tubert-Brohman Brohman,, I.; Lyons, T. M.; Tirado-Rives, J.; Jorgensen, W. L. Search for non-nucleoside nucleoside inhibitors of HIV-1 1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. J. Chem. Inf. Model. 2007, 47,, Barreiro,, G.; Kim, J. T.; Guimaraes,, C. R. W.; Bailey, C. M.; Domaoal,, R. A.; Wang, L.; Anderson, K. S.; Jorgensen, W. L. From docking false-positive to active anti-hiv agent. J. Med. Chem. 2007, 50,,
45 Data Mining and Visualization
46 Spiral View for SAR Interpretation. Smellie,, A. General purpose interactive physico-chemical chemical property exploration. J. Chem. Inf. Model. 2007, 47,,
47 Evaluation of Computational Methods J. Comput.-Aided Mol. Des. 2008, March/April special issue
48 Open Data. Reusable Chemistry DUD A Directory of Useful Decoys
49 Entrez Links and Neighbors Protein 3D Structure VAST Structure Similarity Chemical Structure Similarity PubChem Small Molecules PubMed Literature Protein Sequences Bioactivity Screens Activity Profile Similarity Term Frequency Statistics Source: Steve Bryant
50 Molecular Libraries Roadmap Technology Development Chemical Diversity Assay Development Data production Molecular Libraries Screening Centers Network Data analysis and dissemination Cheminformatics Research Centers Instrumentation Compound Repository Predictive ADMET
51 Conclusion The good news and the bad news
Information Extraction Technologies in Chemistry A Critical Review
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