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

2. Materials prepared by: Sawsan Khuri, Ph.D. and Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q1 2012 Version 7 The RCSB Protein Data Bank

3. Copyright OpenHelix. No use or reproduction without express written consent3 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

4. URL Organisms Copyright OpenHelix. No use or reproduction without express written consent4 Introduction & Credits: www.rcsb.org RCSB PDB to Access: Molecule of the Month Experimental Data Structure Comparisons MyPDB Alerts Many Tools and Resources The RCSB PDB is managed by 2 members of RCSB

5. Copyright OpenHelix. No use or reproduction without express written consent5 RCSB PDB Features: www.rcsb.org widget framework for customized displays Drag areas to desired location help menu Drag areas to desired location

6. click Copyright OpenHelix. No use or reproduction without express written consent6 Help System: POP-OUT or Use & CLOSE Use help system in 2 nd window, or “over” current page Search help, then close to return to RCSB PDB

7. Structure Deposition & Unique PDB Identifiers Copyright OpenHelix. No use or reproduction without express written consent7 PDB ID examples: 2ara 1lr5 1e5s Proline hydroxylase Auxin Binding Protein AraC transcription factor (not case-sensitive)

8. Copyright OpenHelix. No use or reproduction without express written consent8 An Example of a Structure Summary Page β-strands α-helices Biological Assembly – 2 asymmetric units sugar-binding domains loops

9. Copyright OpenHelix. No use or reproduction without express written consent9 More Background Information Link at bottom of homepage

10. Copyright OpenHelix. No use or reproduction without express written consent10 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

11. RCSB PDB Homepage Copyright OpenHelix. No use or reproduction without express written consent11 Top bar search To links & options News area Featured Molecule Featured System Drillable Data Distribution Summaries Latest Structures Header Browse Or Advanced search www.rcsb.org

12. Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent12 Search Categories and examples: All Categories: e.g. PDB ID; molecule name; author Author: e.g. Perutz, MF; smith, j Macromolecule: e.g. Prothrombin; histone Sequence: e.g. vpstaireisllkelkddnivrlydivhsdahk Ligand: e.g. biotin, BTN Additional search options options

13. Copyright OpenHelix. No use or reproduction without express written consent13 All Categories for Transcription Factor Information click Our Query = Transcription factor p65 click

14. Copyright OpenHelix. No use or reproduction without express written consent14 Data Distribution Results Data distribution of hits Molecules of the Month Table of results enlarge Advanced search Save search Query details, including Query in XML format

15. Copyright OpenHelix. No use or reproduction without express written consent15 Search Results Data distribution of hits Molecules of the Month Table of results enlarge Special education features related to query terms List of resulting structures Hyperlinked text Result Options: - Download - view PDB file - structure visualization Display options

16. Search Categories and examples: All Categories: e.g. PDB ID; molecule name; author Author: e.g. Perutz, MF; smith, j Macromolecule: e.g. Prothrombin; histone Sequence: e.g. vpstaireisllkelkddnivrlydivhsdahk Ligand: e.g. biotin, BTN Additional search options Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent16 click Input PDB ID & chain ID or paste Sequence (Protein or nucleotide) Search methods BLAST vs. FASTA: See RCSB PDB Help or OpenHelix tutorials

17. Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent17 Search options click

18. Copyright OpenHelix. No use or reproduction without express written consent18 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

19. Copyright OpenHelix. No use or reproduction without express written consent19 Summary Page Primary Citation One for every structure Organized similarly It provides access to a wealth of data Customizable with a widget framework Re-arranged sections in red Use Reset Layout to return to default Source Ligand Component Experiment Details Deposition Summary Images & Viewing Options Menus Related Entries 2arc Enter 2arc External Data (orange) MyPDB Molecular Description Report tabs Title & ID Images & Viewing Options Molecular Description Primary Citation Source Ligand Component Related Entries External Data (orange) Experiment Details Deposition Summary MyPDB Report tabs Title & ID Menus Reset Layout

20. Copyright OpenHelix. No use or reproduction without express written consent20 Structure Summary Page - Top AraC AND L-arabinose citation reports Title & ID

21. Copyright OpenHelix. No use or reproduction without express written consent21 Structure Summary Page – Top, cont. Larger image “Looking at Structures” Education section Toggle through views Click here Asymmetric Unit options:

22. Copyright OpenHelix. No use or reproduction without express written consent22 Jmol Viewer Mouse over for info & click to display Help tab Scripting box http://jmol.sourceforge.net/ Right click Menus to easily change coloring & display styles

23. Copyright OpenHelix. No use or reproduction without express written consent23 Structure Summary Page - Bottom Source Related PDB Entries Ligand Component External Annotations MyPDB Deposition Summary Experimental Details

24. Ligand Chemical Component - Ligand Explorer Copyright OpenHelix. No use or reproduction without express written consent24

25. Copyright OpenHelix. No use or reproduction without express written consent25 Sequence Tab Graphic of secondary structures Choose domain assignments or annotations from dropdown menu Specify how you want to view graphic Results Tabs Select more annotations References below Set viewing preferences submit

26. Copyright OpenHelix. No use or reproduction without express written consent26 Annotations Report Database links CATH SCOP PFAM SBKB

27. Copyright OpenHelix. No use or reproduction without express written consent27 Sequence Similarity Report

28. Copyright OpenHelix. No use or reproduction without express written consent28 3D Similarity Report Alignment summary Jmol viewer Toggle alignment views Block Conservation Other comparison methods Download & Help

29. Copyright OpenHelix. No use or reproduction without express written consent29 Literature Report Additional PDB entries

30. Copyright OpenHelix. No use or reproduction without express written consent30 Mouse over for details Biology & Chemistry Report Structure Details Protein Details Gene Details

31. Copyright OpenHelix. No use or reproduction without express written consent31 Methods Report Details vary by protein, can include: Crystallization Crystal data Diffraction Refinement data Refinement Software & computing Crystallization Diffraction More sections Crystal data

32. Copyright OpenHelix. No use or reproduction without express written consent32 Color- coded Geometry Report Top Details of bond lengths & angles Middle Lower

33. Copyright OpenHelix. No use or reproduction without express written consent33 Geometry Report Bond Length Table

34. Copyright OpenHelix. No use or reproduction without express written consent34 Links Report Scroll down to SCOP & CATH

35. Copyright OpenHelix. No use or reproduction without express written consent35 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

36. Copyright OpenHelix. No use or reproduction without express written consent36 Additional Homepage Features Next slide RCSB PDB statistics & growth Browse term hierarchies, See associated structures

37. Copyright OpenHelix. No use or reproduction without express written consent37 Advanced Search Form keyword Build elegant, multi-faceted queries Add criteria

38. Copyright OpenHelix. No use or reproduction without express written consent38 Advanced Search Example, Criteria 1 Molecule type Change defaults from “ignore” click

39. Copyright OpenHelix. No use or reproduction without express written consent39 Advanced Search Example, Criteria 2 Experimental Method X-RAY Yes Any = “OR”

40. Copyright OpenHelix. No use or reproduction without express written consent40 Advanced Search Example, Additional Criteria menus # of Entities Has Ligand(s) 5 5

41. Copyright OpenHelix. No use or reproduction without express written consent41 Advanced Search Results Our query PDB Advanced searches = powerful data access tool

42. Copyright OpenHelix. No use or reproduction without express written consent42 Additional Homepage Features, cont.

43. Copyright OpenHelix. No use or reproduction without express written consent43 Latest Release New structure Papers Additional Homepage Features, New Structures Lower on page, FTP archive access

44. Copyright OpenHelix. No use or reproduction without express written consent44 Unreleased Entries Search Query specific structures

45. Copyright OpenHelix. No use or reproduction without express written consent45 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

46. Click on Compare Structures FTP services www.rcsb.org Copyright OpenHelix. No use or reproduction without express written consent46 Tools & Educational Resources

47. Copyright OpenHelix. No use or reproduction without express written consent47 The RCSB PDB Comparison Tool To Expert mode - vary parameters Read more Sequence Structure Example

48. www.rcsb.org Copyright OpenHelix. No use or reproduction without express written consent48 PDB-101: Structural View of Biology “Life is three- dimensional. … PDB-101 offers tools to explore the molecules of biological processes that define life.” Drillable subcategories

49. www.rcsb.org Copyright OpenHelix. No use or reproduction without express written consent49 Navigate to specific topics Detailed introduction and tips for new PDB users PDB-101: Understanding PDB Data

50. www.rcsb.org Copyright OpenHelix. No use or reproduction without express written consent50 PDB-101: Molecule of the Month Full report click to expand topic

51. www.rcsb.org Copyright OpenHelix. No use or reproduction without express written consent51 PDB-101: Educational Resources Available Materials: Posters/Exhibits Website tutorials Animations Activities/lessons Events

52. Copyright OpenHelix. No use or reproduction without express written consent52 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

53. Copyright OpenHelix. No use or reproduction without express written consent53 Summary Intuitive searches Customizable views Tools PDB-101 For education Featured Molecules Drillable data summaries

54. Copyright OpenHelix. No use or reproduction without express written consent54 Summary, cont Topic reports Structure Summary Report

55. Copyright OpenHelix. No use or reproduction without express written consent55 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB: www.rcsb.org

56. Copyright OpenHelix. No use or reproduction without express written consent56