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Cheminformatics
workflows using the
mobile + cloud platform
Dr. Alex M. Clark
October 2013
© 2013 Molecular Materials Infor...
MOLECULAR MATERIALS INFORMATICS

Overview
• Chemical structures
• Mobile apps
• Cloud computing

2
MOLECULAR MATERIALS INFORMATICS

3

3rd Revolution

mainframes
minicomputers

personal computers
portable laptops

mobile ...
MOLECULAR MATERIALS INFORMATICS

4

Two platform stacks
desktop/
laptop

phone/
tablet

file/database
server

web
services
...
MOLECULAR MATERIALS INFORMATICS

5

Delivery
Apps
• User experience

Cloud
• Web API

• Cached data

• Heavy
calculations
...
MOLECULAR MATERIALS INFORMATICS

Challenges
• Mobile user interfaces are completely
different to desktop products
• Expect...
MOLECULAR MATERIALS INFORMATICS

7

App Catalog
Mobile Molecular
DataSheet (MMDS)

Green Solvents

Living Molecules

MolSy...
MOLECULAR MATERIALS INFORMATICS

Drawing Structures
• Cheminformatics requires a user
interface for drawing structures
• I...
MOLECULAR MATERIALS INFORMATICS

Drawing Reactions

• Components: reuse sketcher, iPhone friendly
• Higher level of markup...
MOLECULAR MATERIALS INFORMATICS

Assembling DataSheets
• MMDS: molecular datasheet unit
- molecular structures
- reaction ...
MOLECULAR MATERIALS INFORMATICS

Scaffolds & Substituents

• Scaffold-centric model useful to drug discovery
• SAR Table a...
MOLECULAR MATERIALS INFORMATICS

Searching

• App interfaces for structure searching

12
MOLECULAR MATERIALS INFORMATICS

Calculation
• Structures used to
calculate properties
• Single molecules, or
whole datash...
MOLECULAR MATERIALS INFORMATICS

Importing
• Receive recognised filetypes
-

clipboard
email
web
other apps (IPC)
webservic...
MOLECULAR MATERIALS INFORMATICS

Exporting
• Apps are only as good as their
ability to use the data
• Export actual data u...
MOLECULAR MATERIALS INFORMATICS

Graphics
• Prepare bitmapped graphics for:
- clipboard
- photo roll
- email
• Can incorpo...
MOLECULAR MATERIALS INFORMATICS

Sharing
• Share data publicly or privately
• Upload to a webservice
- store raw data
- dy...
Real world workflow:
searching for new
Tuberculosis drugs
Dr. Alex M. Clark
October 2013
© 2013 Molecular Materials Informa...
MOLECULAR MATERIALS INFORMATICS

Outline
• Workflow is representative of lead discovery
• Searching for new Mycobacterium
t...
MOLECULAR MATERIALS INFORMATICS

TB Mobile
• Curated data for
tuberculosis drugs
• iOS & Android
• CDD, NIAID grant,
Sean ...
MOLECULAR MATERIALS INFORMATICS

A Good Scaffold
• Objective: use the data from TB Mobile to
find a scaffold, then use to i...
MOLECULAR MATERIALS INFORMATICS

Methodology
• Preliminary work done with desktop software: com.mmi
• Fragment TB Mobile s...
MOLECULAR MATERIALS INFORMATICS

Source Materials
• Scaffold:

• Scaffold origin: inhibitor of Glf target
• 87 molecules w...
MOLECULAR MATERIALS INFORMATICS

Importing

• Email attachment to self: open in SAR Table

24
MOLECULAR MATERIALS INFORMATICS

Raw DataSheet

• Just Molecule and Activity...

25
MOLECULAR MATERIALS INFORMATICS

Draw Scaffold

• Select first row
• Use built in sketcher to
draw scaffold

26
MOLECULAR MATERIALS INFORMATICS

Draw Scaffold

• Select first row
• Use built in sketcher to
draw scaffold

26
MOLECULAR MATERIALS INFORMATICS

Substituent Fields

• R-group labels: offer to create fields

27
MOLECULAR MATERIALS INFORMATICS

Scaffold & Molecule

• Need to assign substituents: automatically

28
MOLECULAR MATERIALS INFORMATICS

Scaffold Matching

• Perform single scaffold:molecule match

29
MOLECULAR MATERIALS INFORMATICS

Scaffold Matching

• Perform single scaffold:molecule match

29
MOLECULAR MATERIALS INFORMATICS

Scaffold Matching

• Perform single scaffold:molecule match

29
MOLECULAR MATERIALS INFORMATICS

Bulk Matching

• Duplicate scaffold, match to all molecules

30
MOLECULAR MATERIALS INFORMATICS

Bulk Results

• Only unambiguous results are provided

31
MOLECULAR MATERIALS INFORMATICS

Bulk Results

• Only unambiguous results are provided

31
MOLECULAR MATERIALS INFORMATICS

Symmetry/Degeneracy

• Two possible results: note degeneracy R4,R6

32
MOLECULAR MATERIALS INFORMATICS

Symmetry/Degeneracy

• Two possible results: note degeneracy R4,R6

32
MOLECULAR MATERIALS INFORMATICS

Finishing Assignment
• Single & bulk scaffold matching: semiautomated assignment, human t...
MOLECULAR MATERIALS INFORMATICS

Searching

• Search public databases using template

34
MOLECULAR MATERIALS INFORMATICS

Searching

• Search public databases using template

34
MOLECULAR MATERIALS INFORMATICS

Search Results

• Results come back with scaffolds assigned

35
MOLECULAR MATERIALS INFORMATICS

Sources

• Data from ChemSpider, PubChem, ChEBI
• Includes database links and vendor info...
MOLECULAR MATERIALS INFORMATICS

Importing

• Search results imported in marked-up form

37
MOLECULAR MATERIALS INFORMATICS

Model Building

• Use known activities to build a SAR model

38
MOLECULAR MATERIALS INFORMATICS

Model Application

• Predicted activities shown as coloured wedges

39
MOLECULAR MATERIALS INFORMATICS

Selected Candidates

• Compile a list: predicted activity > 0.8
• Open in Mobile Molecula...
MOLECULAR MATERIALS INFORMATICS

Selected Candidates

• Compile a list: predicted activity > 0.8
• Open in Mobile Molecula...
MOLECULAR MATERIALS INFORMATICS

Sharing by Email

• Very easy to share using email attachments
• Recipient can open on an...
MOLECULAR MATERIALS INFORMATICS

Sharing by Email

• Very easy to share using email attachments
• Recipient can open on an...
MOLECULAR MATERIALS INFORMATICS

Sharing by Email

• Very easy to share using email attachments
• Recipient can open on an...
MOLECULAR MATERIALS INFORMATICS

Sharing via Dropbox

• MMDS can interact with MolSync app
• DataSheets are uploaded & syn...
MOLECULAR MATERIALS INFORMATICS

MolSync & Dropbox

• MolSync app is a chemistry-aware file browser
• Can make use of Dropb...
MOLECULAR MATERIALS INFORMATICS

Lookup FDA Reference

• Open With the Approved Drugs app

44
MOLECULAR MATERIALS INFORMATICS

Approved Drugs

• 1300 structures for FDA-approved drugs
• Reference search by structural...
MOLECULAR MATERIALS INFORMATICS

Matrix View

• Plot structures in a grid: R1 vs R5

46
MOLECULAR MATERIALS INFORMATICS

Matrix View

• Plot structures in a grid: R1 vs R5

46
MOLECULAR MATERIALS INFORMATICS

Matrix + Predictions

• Compounds with unknown activity predicted
shown using wedge style...
MOLECULAR MATERIALS INFORMATICS

Matrix + Hypotheticals

• Empty squares: propose compounds & predict

48
MOLECULAR MATERIALS INFORMATICS

Matrix + Hypotheticals

• Empty squares: propose compounds & predict

48
MOLECULAR MATERIALS INFORMATICS

Proposing Compounds

• Tap on a square: prompt to create partially
defined entry, defining ...
MOLECULAR MATERIALS INFORMATICS

Hypothetical Compound

• New compound added: partial definition
• R2, R3, R4 and R6 unspec...
MOLECULAR MATERIALS INFORMATICS

Lookup in SPRESI

• Use SPRESImobile app to find similar
compounds: looking for a synthesi...
MOLECULAR MATERIALS INFORMATICS

Similar Backbone

• Found a compound with similar core, possible
synthesis template: cons...
MOLECULAR MATERIALS INFORMATICS

Find Reactions

• Lookup synthetic routes: amide condensation
• Open the reaction data in...
MOLECULAR MATERIALS INFORMATICS

Find Reactions

• Lookup synthetic routes: amide condensation
• Open the reaction data in...
MOLECULAR MATERIALS INFORMATICS

Find Reactions

• Lookup synthetic routes: amide condensation
• Open the reaction data in...
MOLECULAR MATERIALS INFORMATICS

Yield101

• Prototype synthetic chemistry lab notebook
• Reaction components imported

54
MOLECULAR MATERIALS INFORMATICS

Reaction Scheme

• Tidyup structures, add in reagent

55
MOLECULAR MATERIALS INFORMATICS

Lookup Starting Material

• Use Mobile Reagents integration to find
commercial source for ...
MOLECULAR MATERIALS INFORMATICS

Lookup in ChemSpider

• Paste into ChemSpider Mobile
app to do structure search
• Open ma...
MOLECULAR MATERIALS INFORMATICS

Lookup in ChemSpider

• Paste into ChemSpider Mobile
app to do structure search
• Open ma...
MOLECULAR MATERIALS INFORMATICS

Quantitative Details

• Enter starting quantity, density: preliminary
estimate of amounts...
MOLECULAR MATERIALS INFORMATICS

Public Sharing

• Upload scheme to molsync.com
• Generates publicly sharable link

59
MOLECULAR MATERIALS INFORMATICS

Shared Content
• Stores chemical data in its
native form:
- molecules
- reaction schemes
...
MOLECULAR MATERIALS INFORMATICS

Shared Content
• Stores chemical data in its
native form:
- molecules
- reaction schemes
...
MOLECULAR MATERIALS INFORMATICS

Numerous Formats
• Sharing site stores pure data, creates preview
graphics dynamically......
MOLECULAR MATERIALS INFORMATICS

62

Vector Graphics
• Quality is perfect at all resolutions: screen,
projector, web, prin...
MOLECULAR MATERIALS INFORMATICS

Microsoft Office Documents
• Independent implementation of OOXML spec
• Embedded graphics ...
MOLECULAR MATERIALS INFORMATICS

SAR Table Documents

• Scaffold/substituent tables for manuscripts

64
MOLECULAR MATERIALS INFORMATICS

Matrix PDF

• Multi-page layout: print directly or email PDF

65
MOLECULAR MATERIALS INFORMATICS

Tweeting
• Can tweet directly from
apps like MMDS
• First upload data to
molsync.com
• Th...
MOLECULAR MATERIALS INFORMATICS

Open Drug Discovery Teams

• Curation of open data, e.g. Twitter & RSS feeds
• Rare & neg...
MOLECULAR MATERIALS INFORMATICS

Harvested Tweet

• Tweet got harvested into Tuberculosis topic
• Inline preview browsed, ...
MOLECULAR MATERIALS INFORMATICS

Chemistry Aware

• The app understands chemical data
• Users can use the data, open with ...
MOLECULAR MATERIALS INFORMATICS

Rinse & Repeat
• Defer to experimentalists: measure activity for
selected compounds with ...
MOLECULAR MATERIALS INFORMATICS

Living Molecules
• Going beyond desktop-era functionality
• Devices have:
-

long battery...
MOLECULAR MATERIALS INFORMATICS

Molecular Glyphs

• Recognition sequence: point camera
• View content, import, manage, ut...
MOLECULAR MATERIALS INFORMATICS

Conclusion
• Cheminformatics workflows historically the role of
specialists: expensive and...
Acknowledgments
• Antony Williams

http://molmatinf.com/venice.html

• Sean Ekins
• Joel Freundlich
• NETTAB / Bioinformat...
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Alex Clark : NETTAB 2013

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Cheminformatics
workflows using the
mobile + cloud platform. Presentation by Dr. Alex M. Clark of Molecular Materials Informatics at the NETTAB 2013 meeting in Venice, Italy. The presentation introduces the significance of mobile apps in science, and the scope of their capabilities in chemical structure informatics. The bulk of the talk describes an account of a preliminary workflow using open science data to search for viable leads for a cure for tuberculosis. The workflow described makes use of a combination of mobile, cloud and conventional desktop-based technology, all stitched together by facile communication, sharing and collaboration features.

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Transcript of "Alex Clark : NETTAB 2013"

  1. 1. Cheminformatics workflows using the mobile + cloud platform Dr. Alex M. Clark October 2013 © 2013 Molecular Materials Informatics, Inc. http://molmatinf.com
  2. 2. MOLECULAR MATERIALS INFORMATICS Overview • Chemical structures • Mobile apps • Cloud computing 2
  3. 3. MOLECULAR MATERIALS INFORMATICS 3 3rd Revolution mainframes minicomputers personal computers portable laptops mobile tablets smartphones • The mobile platform is revolutionary: a clean break - entirely new user interface no backward compatibility highly constrained resources applicable to entirely new situations
  4. 4. MOLECULAR MATERIALS INFORMATICS 4 Two platform stacks desktop/ laptop phone/ tablet file/database server web services compute cluster cloud resources
  5. 5. MOLECULAR MATERIALS INFORMATICS 5 Delivery Apps • User experience Cloud • Web API • Cached data • Heavy calculations • Light calculations • Large data • Sharing • Centralised storage
  6. 6. MOLECULAR MATERIALS INFORMATICS Challenges • Mobile user interfaces are completely different to desktop products • Expectations: functionality, extreme simplicity • Complex interfaces much harder: drawing chemical structures requires redesign • Visualisation is more difficult: screen size • Storage limitations: big data is a problem • Calculations split mobile vs. cloud 6
  7. 7. MOLECULAR MATERIALS INFORMATICS 7 App Catalog Mobile Molecular DataSheet (MMDS) Green Solvents Living Molecules MolSync SAR Table MolPrime+ MolPrime Lab Solvents Approved Drugs Reaction101 Yield101 SPRESImobile Open Drug Discovery Teams TB Mobile ChemSpider
  8. 8. MOLECULAR MATERIALS INFORMATICS Drawing Structures • Cheminformatics requires a user interface for drawing structures • Interface needs to be: - capable for complex structures publication quality fast to use phone-size form factor • Traditional interface paradigm on touchscreen: unusable... 8
  9. 9. MOLECULAR MATERIALS INFORMATICS Drawing Reactions • Components: reuse sketcher, iPhone friendly • Higher level of markup useful for lab notebooks • Used by MMDS, Reaction101, Yield101 9
  10. 10. MOLECULAR MATERIALS INFORMATICS Assembling DataSheets • MMDS: molecular datasheet unit - molecular structures - reaction schemes - scalar data (text, numbers) • Table-like structure, roughly equivalent to SDfile/RDfile • Operate on individual rows or whole datasheets 10
  11. 11. MOLECULAR MATERIALS INFORMATICS Scaffolds & Substituents • Scaffold-centric model useful to drug discovery • SAR Table app: optimised for data entry • And: analysis, visualisation and calculation 11
  12. 12. MOLECULAR MATERIALS INFORMATICS Searching • App interfaces for structure searching 12
  13. 13. MOLECULAR MATERIALS INFORMATICS Calculation • Structures used to calculate properties • Single molecules, or whole datasheets • Simple calculations: done by app • Difficult calculations: use webservice 13
  14. 14. MOLECULAR MATERIALS INFORMATICS Importing • Receive recognised filetypes - clipboard email web other apps (IPC) webservices remote filesystems • Documented formats, e.g. SketchEl, MDL, ChemDraw, CML 14
  15. 15. MOLECULAR MATERIALS INFORMATICS Exporting • Apps are only as good as their ability to use the data • Export actual data using cheminformatics formats - clipboard email web sharing twitter webservices remote filesystems 15
  16. 16. MOLECULAR MATERIALS INFORMATICS Graphics • Prepare bitmapped graphics for: - clipboard - photo roll - email • Can incorporate into other apps on the device (e.g. Keynote) • Vector graphics: SVG, EPS, Microsoft Word & Excel 16
  17. 17. MOLECULAR MATERIALS INFORMATICS Sharing • Share data publicly or privately • Upload to a webservice - store raw data - dynamically render - hosted by molsync.com • Tweet directly from the app: share the link 17
  18. 18. Real world workflow: searching for new Tuberculosis drugs Dr. Alex M. Clark October 2013 © 2013 Molecular Materials Informatics, Inc. http://molmatinf.com
  19. 19. MOLECULAR MATERIALS INFORMATICS Outline • Workflow is representative of lead discovery • Searching for new Mycobacterium tuberculosis drugs • Open data, open science, collaborating with experimentalists • Workflow involves: http://molmatinf.com/ venice.html - mobile apps - cloud-based webservices - traditional software 19
  20. 20. MOLECULAR MATERIALS INFORMATICS TB Mobile • Curated data for tuberculosis drugs • iOS & Android • CDD, NIAID grant, Sean Ekins • App presents a browseable list of structures • Can filter by target, sort by structural similarity • Visual data exportable.... 20
  21. 21. MOLECULAR MATERIALS INFORMATICS A Good Scaffold • Objective: use the data from TB Mobile to find a scaffold, then use to infer gene target from a larger collection of SAR data • What makes a good scaffold? 21
  22. 22. MOLECULAR MATERIALS INFORMATICS Methodology • Preliminary work done with desktop software: com.mmi • Fragment TB Mobile structures, scaffold-like • Perform scaffold-substructure vs. 7000 in vitro • Derive R-groups, tidy, present graphically, browse... http://molmatinf.com/venice.html 22
  23. 23. MOLECULAR MATERIALS INFORMATICS Source Materials • Scaffold: • Scaffold origin: inhibitor of Glf target • 87 molecules with in vitro activity (yes/no) • Scaffold seems to elicit an activity pattern • Next step: load it into the app ecosystem... 23
  24. 24. MOLECULAR MATERIALS INFORMATICS Importing • Email attachment to self: open in SAR Table 24
  25. 25. MOLECULAR MATERIALS INFORMATICS Raw DataSheet • Just Molecule and Activity... 25
  26. 26. MOLECULAR MATERIALS INFORMATICS Draw Scaffold • Select first row • Use built in sketcher to draw scaffold 26
  27. 27. MOLECULAR MATERIALS INFORMATICS Draw Scaffold • Select first row • Use built in sketcher to draw scaffold 26
  28. 28. MOLECULAR MATERIALS INFORMATICS Substituent Fields • R-group labels: offer to create fields 27
  29. 29. MOLECULAR MATERIALS INFORMATICS Scaffold & Molecule • Need to assign substituents: automatically 28
  30. 30. MOLECULAR MATERIALS INFORMATICS Scaffold Matching • Perform single scaffold:molecule match 29
  31. 31. MOLECULAR MATERIALS INFORMATICS Scaffold Matching • Perform single scaffold:molecule match 29
  32. 32. MOLECULAR MATERIALS INFORMATICS Scaffold Matching • Perform single scaffold:molecule match 29
  33. 33. MOLECULAR MATERIALS INFORMATICS Bulk Matching • Duplicate scaffold, match to all molecules 30
  34. 34. MOLECULAR MATERIALS INFORMATICS Bulk Results • Only unambiguous results are provided 31
  35. 35. MOLECULAR MATERIALS INFORMATICS Bulk Results • Only unambiguous results are provided 31
  36. 36. MOLECULAR MATERIALS INFORMATICS Symmetry/Degeneracy • Two possible results: note degeneracy R4,R6 32
  37. 37. MOLECULAR MATERIALS INFORMATICS Symmetry/Degeneracy • Two possible results: note degeneracy R4,R6 32
  38. 38. MOLECULAR MATERIALS INFORMATICS Finishing Assignment • Single & bulk scaffold matching: semiautomated assignment, human tiebreakers • Have 87 compounds, 21 active against TB • Based on scaffold from a binder of Glf enzyme (essential for mycobacterial growth) • What next? • Look for other compounds: same scaffold 33
  39. 39. MOLECULAR MATERIALS INFORMATICS Searching • Search public databases using template 34
  40. 40. MOLECULAR MATERIALS INFORMATICS Searching • Search public databases using template 34
  41. 41. MOLECULAR MATERIALS INFORMATICS Search Results • Results come back with scaffolds assigned 35
  42. 42. MOLECULAR MATERIALS INFORMATICS Sources • Data from ChemSpider, PubChem, ChEBI • Includes database links and vendor information 36
  43. 43. MOLECULAR MATERIALS INFORMATICS Importing • Search results imported in marked-up form 37
  44. 44. MOLECULAR MATERIALS INFORMATICS Model Building • Use known activities to build a SAR model 38
  45. 45. MOLECULAR MATERIALS INFORMATICS Model Application • Predicted activities shown as coloured wedges 39
  46. 46. MOLECULAR MATERIALS INFORMATICS Selected Candidates • Compile a list: predicted activity > 0.8 • Open in Mobile Molecular DataSheet (MMDS) app 40
  47. 47. MOLECULAR MATERIALS INFORMATICS Selected Candidates • Compile a list: predicted activity > 0.8 • Open in Mobile Molecular DataSheet (MMDS) app 40
  48. 48. MOLECULAR MATERIALS INFORMATICS Sharing by Email • Very easy to share using email attachments • Recipient can open on any device, including mobile 41
  49. 49. MOLECULAR MATERIALS INFORMATICS Sharing by Email • Very easy to share using email attachments • Recipient can open on any device, including mobile 41
  50. 50. MOLECULAR MATERIALS INFORMATICS Sharing by Email • Very easy to share using email attachments • Recipient can open on any device, including mobile 41
  51. 51. MOLECULAR MATERIALS INFORMATICS Sharing via Dropbox • MMDS can interact with MolSync app • DataSheets are uploaded & synchronised in Dropbox 42
  52. 52. MOLECULAR MATERIALS INFORMATICS MolSync & Dropbox • MolSync app is a chemistry-aware file browser • Can make use of Dropbox's collaboration features 43
  53. 53. MOLECULAR MATERIALS INFORMATICS Lookup FDA Reference • Open With the Approved Drugs app 44
  54. 54. MOLECULAR MATERIALS INFORMATICS Approved Drugs • 1300 structures for FDA-approved drugs • Reference search by structural similarity 45
  55. 55. MOLECULAR MATERIALS INFORMATICS Matrix View • Plot structures in a grid: R1 vs R5 46
  56. 56. MOLECULAR MATERIALS INFORMATICS Matrix View • Plot structures in a grid: R1 vs R5 46
  57. 57. MOLECULAR MATERIALS INFORMATICS Matrix + Predictions • Compounds with unknown activity predicted shown using wedge style 47
  58. 58. MOLECULAR MATERIALS INFORMATICS Matrix + Hypotheticals • Empty squares: propose compounds & predict 48
  59. 59. MOLECULAR MATERIALS INFORMATICS Matrix + Hypotheticals • Empty squares: propose compounds & predict 48
  60. 60. MOLECULAR MATERIALS INFORMATICS Proposing Compounds • Tap on a square: prompt to create partially defined entry, defining R1 and R5 49
  61. 61. MOLECULAR MATERIALS INFORMATICS Hypothetical Compound • New compound added: partial definition • R2, R3, R4 and R6 unspecified 50
  62. 62. MOLECULAR MATERIALS INFORMATICS Lookup in SPRESI • Use SPRESImobile app to find similar compounds: looking for a synthesis... 51
  63. 63. MOLECULAR MATERIALS INFORMATICS Similar Backbone • Found a compound with similar core, possible synthesis template: consult literature 52
  64. 64. MOLECULAR MATERIALS INFORMATICS Find Reactions • Lookup synthetic routes: amide condensation • Open the reaction data in Yield101 53
  65. 65. MOLECULAR MATERIALS INFORMATICS Find Reactions • Lookup synthetic routes: amide condensation • Open the reaction data in Yield101 53
  66. 66. MOLECULAR MATERIALS INFORMATICS Find Reactions • Lookup synthetic routes: amide condensation • Open the reaction data in Yield101 53
  67. 67. MOLECULAR MATERIALS INFORMATICS Yield101 • Prototype synthetic chemistry lab notebook • Reaction components imported 54
  68. 68. MOLECULAR MATERIALS INFORMATICS Reaction Scheme • Tidyup structures, add in reagent 55
  69. 69. MOLECULAR MATERIALS INFORMATICS Lookup Starting Material • Use Mobile Reagents integration to find commercial source for starting material 56
  70. 70. MOLECULAR MATERIALS INFORMATICS Lookup in ChemSpider • Paste into ChemSpider Mobile app to do structure search • Open matching ChemSpider compound information page 57
  71. 71. MOLECULAR MATERIALS INFORMATICS Lookup in ChemSpider • Paste into ChemSpider Mobile app to do structure search • Open matching ChemSpider compound information page 57
  72. 72. MOLECULAR MATERIALS INFORMATICS Quantitative Details • Enter starting quantity, density: preliminary estimate of amounts used in synthesis 58
  73. 73. MOLECULAR MATERIALS INFORMATICS Public Sharing • Upload scheme to molsync.com • Generates publicly sharable link 59
  74. 74. MOLECULAR MATERIALS INFORMATICS Shared Content • Stores chemical data in its native form: - molecules - reaction schemes - datasheets • Can share, tweet, etc. • Download data in many different forms... 60
  75. 75. MOLECULAR MATERIALS INFORMATICS Shared Content • Stores chemical data in its native form: - molecules - reaction schemes - datasheets • Can share, tweet, etc. • Download data in many different forms... 60
  76. 76. MOLECULAR MATERIALS INFORMATICS Numerous Formats • Sharing site stores pure data, creates preview graphics dynamically... and interconversions Molecules • SketchEl • MDL MOL • CML Reactions • DataSheet XML • MDL RXN • MDL RDF Collections • DataSheet XML • MDL SDfile Raster Graphics • PNG • PNG ZIP Vector Graphics • SVG • SVG ZIP • HTML SVG • EPS • MS Word • MS Excel 61
  77. 77. MOLECULAR MATERIALS INFORMATICS 62 Vector Graphics • Quality is perfect at all resolutions: screen, projector, web, printer, PDF... Vector Bitmap
  78. 78. MOLECULAR MATERIALS INFORMATICS Microsoft Office Documents • Independent implementation of OOXML spec • Embedded graphics use vector DrawingML 63
  79. 79. MOLECULAR MATERIALS INFORMATICS SAR Table Documents • Scaffold/substituent tables for manuscripts 64
  80. 80. MOLECULAR MATERIALS INFORMATICS Matrix PDF • Multi-page layout: print directly or email PDF 65
  81. 81. MOLECULAR MATERIALS INFORMATICS Tweeting • Can tweet directly from apps like MMDS • First upload data to molsync.com • Then emit tweet with link • Observe list of predefined hashtags: #tuberculosis 66
  82. 82. MOLECULAR MATERIALS INFORMATICS Open Drug Discovery Teams • Curation of open data, e.g. Twitter & RSS feeds • Rare & neglected diseases, precompetitive areas 67
  83. 83. MOLECULAR MATERIALS INFORMATICS Harvested Tweet • Tweet got harvested into Tuberculosis topic • Inline preview browsed, with other thumbnails 68
  84. 84. MOLECULAR MATERIALS INFORMATICS Chemistry Aware • The app understands chemical data • Users can use the data, open with in apps... 69
  85. 85. MOLECULAR MATERIALS INFORMATICS Rinse & Repeat • Defer to experimentalists: measure activity for selected compounds with predictions • Return to SAR Table app: - provide activity results visualise matrix plot with actual data added rebuild model, regenerate predictions iteratively refine hypothesis • Done using $50 worth of software and tablet • Workflow is appropriate for use by experimentalists 70
  86. 86. MOLECULAR MATERIALS INFORMATICS Living Molecules • Going beyond desktop-era functionality • Devices have: - long battery life bluetooth location awareness camera! • Observe the strange symbol: molecular glyph 71
  87. 87. MOLECULAR MATERIALS INFORMATICS Molecular Glyphs • Recognition sequence: point camera • View content, import, manage, utilise, export 72
  88. 88. MOLECULAR MATERIALS INFORMATICS Conclusion • Cheminformatics workflows historically the role of specialists: expensive and/or complex • Mobile apps are much cheaper and much more accessible to experimentalists • Mobile+cloud can: - replace simple-to-medium tasks - coexist with complex tasks run on desktop software • Other advantages: - anywhere/anytime portability - excellent collaboration and sharing - non-existent installation or maintenance burden 73
  89. 89. Acknowledgments • Antony Williams http://molmatinf.com/venice.html • Sean Ekins • Joel Freundlich • NETTAB / Bioinformatics Italian Society • InfoChem, Eidogen-Sertanty • Inquiries to info@molmatinf.com http://molmatinf.com http://molsync.com http://cheminf20.org @aclarkxyz
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