1. Copyright OpenHelix. No use or reproduction without express written consent1

2. PSI SBKB The Structural Biology Knowledgebase by Protein Structure Initiative (PSI) and Nature Publishing Group (NPG) Materials prepared by: Jennifer Williams, Ph.D. www.openhelix.com Version 3

3. Copyright OpenHelix. No use or reproduction without express written consent3 PSI SBKB Agenda Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises PSI SBKB: http://sbkb.org/

4. Copyright OpenHelix. No use or reproduction without express written consent4 SB update search sign up navigation PSI SBKB Homepage “This ‘one-stop shop’ provides users with the available genetic, structural, functional and experimental information about a particular protein of interest.”

5. Copyright OpenHelix. No use or reproduction without express written consent5 PSI SBKB Left Navigation Next section Next slides Access content hubs organized by scientific focus

6. FAQs Download Tour tutorial by OpenHelix Interactive tutorial by SBKB Copyright OpenHelix. No use or reproduction without express written consent6 About PSI SBKB Click “NPG is the scientific publishing arm of Macmillan Publishers Ltd, … The Editors at Nature Publishing Group appreciate the central importance of structural biology research to molecular and cell biology as well as therapeutic development.” “… is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure.” www.nigms.nih.gov/Initiatives/PSI

7. Copyright OpenHelix. No use or reproduction without express written consent7 PSI SBKB Overview Image - http://sbkb.org/about/getting_started.html PSI Portals & Resources Biological Resources PSI SBKB: central bridge

8. Copyright OpenHelix. No use or reproduction without express written consent8 About PSI SBKB http://www.springerlink.com/content/u703350780u34550/ Publications

9. Copyright OpenHelix. No use or reproduction without express written consent9 PSI SBKB Agenda Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises PSI SBKB: http://sbkb.org/

10. Copyright OpenHelix. No use or reproduction without express written consent10 Structural Biology Update research advances featured system news events

11. Copyright OpenHelix. No use or reproduction without express written consent11 Research Advances Research Advances:  editorials by Nature Publishing Group  structure related articles from various journals, including Nature journals

12. Copyright OpenHelix. No use or reproduction without express written consent12 Featured System Structure search references

13. Copyright OpenHelix. No use or reproduction without express written consent13 Other Structural Biology Update Features

14. Copyright OpenHelix. No use or reproduction without express written consent14 Accessing Structural Biology Update Features search for more info in the SBKB click

15. Copyright OpenHelix. No use or reproduction without express written consent15 PSI SBKB Agenda Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises PSI SBKB: http://sbkb.org/

16. Copyright OpenHelix. No use or reproduction without express written consent16 PSI SBKB Content Organized into Hubs Content Hubs: Targets Protein Structures, Sequences & Functions Membrane Proteins Homology Models Methods Hubs = Organized by Scientific Focus for Ease of Use

17. Copyright OpenHelix. No use or reproduction without express written consent17 Targets Hub Quick TargetTrack search 1 st target result

18. Copyright OpenHelix. No use or reproduction without express written consent18 Targets Hub, cont. Register Log in

19. Copyright OpenHelix. No use or reproduction without express written consent19 Membrane Proteins Hub Membrane Proteins Hub:  Research Highlights  PSI Membrane Network  Human TM Proteome DB  MPStruc for 3D structures  Nominate Proteins  Find New Technologies

20. Copyright OpenHelix. No use or reproduction without express written consent20 Methods Hub Methods Hub Versions:  Technical Highlights  TargetTrack access  Tech Portal Searches Additional Resources:  Publication Portal  Order PSI Clones  Synchrotron Info

21. Copyright OpenHelix. No use or reproduction without express written consent21 PSI SBKB Agenda Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises PSI SBKB: http://sbkb.org/

22. Copyright OpenHelix. No use or reproduction without express written consent22 PSI SBKB Search Form search click help

23. Copyright OpenHelix. No use or reproduction without express written consent23 Sequence Search Results Search type Search input Result summary click

24. Glossary Copyright OpenHelix. No use or reproduction without express written consent24 Structures Report navigation click

25. Copyright OpenHelix. No use or reproduction without express written consent25 Structure Viewer Many visualization options for exploring your protein! Image Controls Image Notes Image of Structure

26. Copyright OpenHelix. No use or reproduction without express written consent26 Structure Annotation Reports, Gene-Level View Navigation area Primary sources Additional info Other informational views Model organism database

27. Copyright OpenHelix. No use or reproduction without express written consent27 Sequence accessions Protein sequence Structure Annotation Reports, Other Views

28. Copyright OpenHelix. No use or reproduction without express written consent28 Pre-Released Report Full info upon release

29. Copyright OpenHelix. No use or reproduction without express written consent29 Models Report Model quality influenced by:  Template flexibility & variation  Methodology limitations  Evolutionary distances

30. Copyright OpenHelix. No use or reproduction without express written consent30 Query PMP Report Matches Select models or structures for comparisons Superposition image

31. Copyright OpenHelix. No use or reproduction without express written consent31 Targets & Protocols Report navigation Next slide

32. Copyright OpenHelix. No use or reproduction without express written consent32 Targets & Protocols Report, cont.

33. Copyright OpenHelix. No use or reproduction without express written consent33 Materials Report

34. Copyright OpenHelix. No use or reproduction without express written consent34 Structure (PDB ID) Search PDB ID = very specific, only single result!

35. Copyright OpenHelix. No use or reproduction without express written consent35 UniProt Accession Search UniProt Accession: may be associated with multiple PDB structures PDB hits

36. Copyright OpenHelix. No use or reproduction without express written consent36 PSI SBKB Agenda Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises PSI SBKB: http://sbkb.org/

37. SBKB homepage: http://sbkb.org/ Copyright OpenHelix. No use or reproduction without express written consent37 Text Searches by text

38. Copyright OpenHelix. No use or reproduction without express written consent38 SBKB Gateway Results

39. Copyright OpenHelix. No use or reproduction without express written consent39 PSI Sites Results

40. Copyright OpenHelix. No use or reproduction without express written consent40 Annotation Results CATH results

41. Copyright OpenHelix. No use or reproduction without express written consent41 Methods Results PubMed Central

42. Copyright OpenHelix. No use or reproduction without express written consent42 Tech Report Results Technology Portal PSI Center Technology Summary Description Contact Publication Figures

43. Copyright OpenHelix. No use or reproduction without express written consent43 Structures and Annotations KB-Rank Results KB-Ranked Results

44. Copyright OpenHelix. No use or reproduction without express written consent44 KB-Rank Search Tool Example: Asthma click Search term asthma click SBKB report

45. Copyright OpenHelix. No use or reproduction without express written consent45 PSI SBKB Agenda PSI SBKB: http://sbkb.org/ Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises

46. Copyright OpenHelix. No use or reproduction without express written consent46 Additional Features evaluate or propose your amino acid sequences help characterize novel protein sequences see stats on PSI progress sources of additional information next

47. Copyright OpenHelix. No use or reproduction without express written consent47 Publications Access to many PSI articles

48. evaluate your amino acid sequences Copyright OpenHelix. No use or reproduction without express written consent48 Right Side: Analyze Sequences

49. notice Copyright OpenHelix. No use or reproduction without express written consent49 Right Side: Analyze Sequences - Results

50. Copyright OpenHelix. No use or reproduction without express written consent50 Right Side: Analyze Sequences – Results, cont.

51. Copyright OpenHelix. No use or reproduction without express written consent51 Functional Sleuth

52. Copyright OpenHelix. No use or reproduction without express written consent52 Functional Sleuth, cont. Mouse over for information Right click to view structures Click to progress through Taxonomy Tree PDB ID search

53. PSI Metrics Copyright OpenHelix. No use or reproduction without express written consent53 Latest PSI Statistics New Structures Developmental Datasets

54. Copyright OpenHelix. No use or reproduction without express written consent54 Other Entry Points to the SBKB: UniProt Pages Cross-references click

55. Copyright OpenHelix. No use or reproduction without express written consent55 Other Entry Points: RCSB PDB & NCBI Pages http://www.pdb.org/pdb/explore/explore.do?pdbId=2PE2 http://www.ncbi.nlm.nih.gov/protein/2PE2_A

56. Copyright OpenHelix. No use or reproduction without express written consent56 PSI SBKB Agenda PSI SBKB: http://sbkb.org/ Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises

57. Copyright OpenHelix. No use or reproduction without express written consent57 PSI SBKB: Bridge to So Much Information! SBKB: a Bridge between Biological and PSI Structural Information PSI Resources Biological Resources SBKB

58. Copyright OpenHelix. No use or reproduction without express written consent58 PSI SBKB: Structural Biology Update  Includes:  Research advances  Featured System  News  Events  And more!

59. Copyright OpenHelix. No use or reproduction without express written consent59 PSI SBKB: Sequence and Structure Searches Summary Reports Detailed Results

60. Copyright OpenHelix. No use or reproduction without express written consent60 PSI SBKB: Text Searches Access to Structures and Annotations Ranked by Relevance! KB-Rank Results

61. Copyright OpenHelix. No use or reproduction without express written consent61 PSI SBKB: Additional Features

62. Copyright OpenHelix. No use or reproduction without express written consent62 PSI SBKB Agenda PSI SBKB: http://sbkb.org/ Introduction and Credits Structural Biology Update Content Hubs Sequence or Structure Search Text Searches Additional Features Summary Exercises

63. Copyright OpenHelix. No use or reproduction without express written consent63