1. Demo: Protein Information Resource
October 10, 2003
NIH Proteomics Workshop
Bethesda, MD
Raja Mazumder, Ph.D.
Scientific Coordinator and Senior Protein Scientist, PIR

2. Database Demo NREF Database
NREF Entry (NF )
iProClass Database
iProClass Sequence (A58910), Motif (PCM00487)
PIR-PSD Database
PIR Entry (A58910)
Other Molecular Databases
Function: KEGG Enzyme (EC ), KEGG Pathway (MAP00230); BRENDA (EC )
Structure: PDB (1AK5), SCOP (Alanine Racemase), CATH (1AK5)
Domain: Pfam (PF00478), CDD (HemL)
Classification: COGs (COG0001)

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

4. Text Search Result

5. Text Search Result with NULL/NOT NULL

6. Peptide Search Results

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

8. PIR-NREF Search Result (II)

9. PIR Pattern Search

10. PIR Pattern Search Result (I)
Pattern Match: Sequence vs. PROSITE

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

12. PIR Domain Display

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

14. PIR-NREF Report

15. Related Sequences

16. PIR-iProClass Database

17. iProClass Sequence Report

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

19. Development of protein sequence databases
Atlas of protein sequence and structure – Dayhoff (1966) first sequence database (pre-bioinformatics). Currently known as Protein Information Resource (PIR)
Protein data bank (PDB) – structural database (1972) remains most widely used database of structures
SWISSPROT – protein sequence database (1987) still in use – not exhaustive but heavily annotated
UniProt: The United Protein Databases (UniProt, 2003) will create a central database of protein sequence and function by joining the forces of the SWISS-PROT, TrEMBL and PIR protein database activities

20. Protein Family Classification
Discovery of New Knowledge by
Using Information Embedded within
Families of Homologous Sequences and Their Structures
Superfamily and Domain 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
Classification allows new identifications that predict functional properties of genome-derived sequences, as well as correcting errors, and providing a framework for organizing sequence space.

21. Protein Family/Superfamily Definitions
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 ?%
Superfamily
A Set of Protein Families That Share a Common Evolutionary Ancestor From End-to-end
Have the Same Domain Architecture
Best-hit rule
Closely related sequences – usually at least 50% identical in sequence and about the same length -- are grouped into families. These proteins are expected to have very similar structure, activity, and properties.
A superfamily may consist of several or many families. Structures are recognizably similar, but functional properties and catalytic activities can differ.

22. Protein Domain Definition
Domains can be described as discrete structurally conserved units in proteins that are evolutionary mobile
They typically correspond to discrete globular folding units in the structure of a protein and may often occur independently of other domains in the protein
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.

23. Network structure of protein classification
P-loop NTPase (Structural fold)
Domain superfamilies
AAA+ ATPases
DNA pumping ATPases
RecA/SF1/SF2 helicase lineage
Homeomorphic families
Replicative DNA helicase
ATPase
Nucleic acid helicase
VACa-D5Rb
MCV-MC094R
SFV-gp080R
FPV-FPV058
MSV-MSV089
AMV-AMV087
VAC-A32L
MCV-MC140L
SFV-gp120L
FPV-FPV197
MSV-MSV171
AMV-AMV150
VAC-A18R
MCV-MC123R
SFV-gp108R
FPV-FPV183
MSV-MSV148
AMV-AMV059

24. Network structure of protein classification

25. Superfamily-Domain-Motif Relationship
Here, for example, are diagrammatic representations of 5 superfamilies containing the calcineurin-like phosphoesterase domain, in several cases in association with other known types of domains.

26. iProClass Superfamily List
All Superfamilies Containing PF00001
Superfamily-Domain Relationship: ~6000 SFs have >=1 Domains
Superfamily for Domain Architecture
Provide more annotation and select seeds for the 6000 SFs for initial interpro xref
SF assignment: based on global score and domain match

27. iProClass Superfamily Report

28. Alignment and Tree View

29. PIR-Protein Sequence Database

30. PIR-PSD Entry

31. BLAST/FASTA Search

32. PIR FASTA Search Result

33. PIR Searches and Alignment
BLAST Search
PIR Searches and Alignment
Multiple Alignment
& Tree View

34. PIR Hidden Markov Model
HMM Model Building & Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM

35. PIR Bibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization

36. PIR Bibliography Submission

37. Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database

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

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

40. PIR Batch retrieval

41. PIR Batch Retrieval Results

42. Pairwise Alignments

43. PIR Pairwise Alignment

44. Composition & Molecular Weight Calculation

45. Composition & Molecular Weight Calculation

46. PIR support center