1. March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information Resource

2. 2 Database Demo NREF Database http://pir.georgetown.edu/pirwww/search/pirnref.shtml iProClass Database http://pir.georgetown.edu/iproclass.html iProClass Sequence (A58910), Motif (PCM00487)A5PCM00487 PIR-PSD Database http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?&uid=A58910 PIR Entry (A58910) Other Molecular Databases Function: KEGG Enzyme (EC 1.1.1.205), KEGG Pathway (MAP00230); BRENDA (EC 1.1.1.205)EC 1.1.1.205MAP00230EC 1.1.1.205 Structure: PDB (1AK5), SCOP (1.003.001.006.002.002), CATH (1AK5)1AK51.003.001.006.002.0021AK5 Family: Pfam (PF00478), BLOCKS (BL00487), PROSITE (PS00487)PF00478BL00487PS00487

3. 3 PIR Web Site (http://pir.georgetown.edu)

4. 4 Text Search Result with NULL/NOT NULL

5. 5 Peptide Search Results

6. 6 PIR-NREF Search Result (I) Test Sequence: ftp://nbrfa.georgetown.edu/pir/misc/test.seq

7. 7 PIR-NREF Search Result (II)

8. 8 HMM Domain/Motif Search

9. 9 PIR Pattern Search

10. 10 PIR Pattern Search Result (I) http://pir.georgetown.edu/pirwww/search/patmatch.html Pattern Match: Sequence vs. PROSITE

11. 11 PIR Pattern Search Result (II) Search a query pattern against a sequence database.

12. 12 PIR Domain Display

13. 13 PIR-NREF Database (http://pir.georgetown.edu/pirwww/search/pirnref.shtml). search

14. 14 PIR-NREF Report

15. 15 PIR-iProClass Database

16. 16 iProClass Sequence Report

17. 17 PDB Structure of Molecule: Inosine- 5'-Monophosphate Dehydrogenase

18. 18 Related Sequences

19. 19 Protein Family Classification Superfamily, Domain, and Motif Classification Superfamily Concept End-to-End Similarity & Same Overall Domain Architecture Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution, Genomics and Proteomics Research Discovery of New Knowledge by Using Information Embedded within Families of Homologous Sequences and Their Structures

20. 20 Protein Family/Superfamily Definitions Family A Set of Protein Sequences That Share a Common Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods) Have the Same Domain Architecture (Except Incomplete or Alternately Spliced) Overall Sequence Identity >=45% Superfamily A Set of Protein Families That Share a Common Evolutionary Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity >=20%

21. 21 Protein Domain Definition Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in >= 2 Superfamilies) A Sequence Can Belong to Only One Protein Family and Superfamily, but May Contain More Than One Domains.

22. 22 Superfamily-Domain-Motif Relationship

23. 23 iProClass Superfamily List All Superfamilies Containing PF00001 Superfamily-Domain Relationship: ~6000 SFs have >=1 Domains Superfamily for Domain Architecture

24. 24 iProClass Superfamily Report

25. 25 Alignment and Tree View

26. 26 PIR-Protein Sequence Database

27. 27 PIR-PSD Entry

28. 28 BLAST/FASTA Search

29. 29 PIR FASTA Search Result

30. 30 PIR Searches and Aligment BLAST Search Multiple Alignment & Tree View

31. 31 PIR Hidden Markov Model http://pir.georgetown.edu/pirwww/search/pirhmm.htmlpirhmm.html HMM Model Building & Sequence Search One Protein Against All HMMs All Proteins Against One HMM

32. 32

33. 33 Bibliography Submission View Bibliography Information View Protein Entry Submit Citation with Optional Categorization S1

34. 34 Bibliography Information Display (I) From PIR-NREF From Other Curated Database (e.g., SGD)

35. 35 Bibliography Information Display (II) From User Submission From Computer- Mapping (e.g. Gene Symbol)

36. 36 Oracle Demo Java Web Interface for Oracle Database Search: (http://pir.georgetown.edu/iproclass.html) WebDB Interface to Oracle (WebDB)WebDB Tables/Views/Objects Functions/Procedures/Packages

37. 37 Proteomic Bioinformatics Large-Scale Analysis of Proteomic Data: Homology Search for Pathways