The document discusses the collaborative and open processing of drug discovery data using open notebook science methodologies, emphasizing full transparency in research. It highlights the use of web 2.0 tools like blogs, wikis, and collaborative platforms to share experimental data and results among researchers. The document includes various links and tools for drug design, cheminformatics, and educational resources, showcasing an innovative approach to scientific research and collaboration.

1. Processing drug discovery raw data collaboratively and openly using Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University August 20, 2008 American Chemical Society

2. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING

3. Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

4. BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD

5. Where’s the Beef?

6. Link to Lab Notebook Page in Wiki

7. Link to Molecules

8. Link to Docking Procedure (Rajarshi Guha)

9. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)

10. Procedure Section

11. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)

12. Using ChemSpider to archive compound characterization

13. ChemSpider predicted vs. experimental NMRs

14. The Most Important Section! The Log

15. Conclusion is Fully Supported

16. Table of Contents

17. Indexing the Experiments in Google

18. Searching with Google Custom Search

19. How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific Compounds Experimental Conditions

20. How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database Educational Big Picture

21. How Should Open Notebook Science be Used?

28. How did this experiment evolve? Third party timestamp

29. http://usefulchem.wikispaces.com/page/diff/Exp037/1577428

34. http://usefulchem.wikispaces.com/SO+Research+Report

35. Comparing Experiments Ugi Master Table

36. YouTube for demonstrating experimental set-up

37. Older Males Prefer Organic Chemistry!

38. Mailing List Facilitates inter-group collaboration

39. Outcome of Guha-Bradley-Rosenthal collboration

40. Collaborative Drug Discovery (CDD) Database

42. Interacting with NMR spectra (JCAMP-DX) in Second Life

43. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)

44. Using ExcelVBA to automate kinetics analysis

45. Reaction profile plotted automatically

46. 3D molecules in Second Life

47. Imine Formation Mechanism: talk to the molecules!

48. Gus Rosania’s Notebook

49. Cameron Neylon’s Notebook

50. Results in Machine-Friendly Format

51. Mettler-Toledo MiniMapper

52. Mettler-Toledo MiniBlock System

53. GoogleDoc to program and report

54. XML reports from MiniMapper robot

55. Methanol 0.4M xs of imine best

56. Where is Science headed? WE ARE HERE

57. Conclusion Communicate first Standardize second In a Science2.0 world redundancy is king