1. Tutorial: Bioinformatics Resources(
Bio-Trac 25 (Proteomics: Principles and Methods)
October 3, 2008
Zhang-Zhi Hu, M.D.
Research Associate Professor
Protein Information Resource, Department of
Biochemistry and Molecular & Cellular Biology
Georgetown University Medical Center

2. Lab:
Protein Examples
Rabbit alpha crystallin A (UniProtKB: CRYAA_RABIT/P02493)
Delta crystallin II (Argininosuccinate lyase) (ARLY2_ANAPL/P24058)
Any additional proteins of your interest for search and retrieval

3. Lab Overview Database Contents, Search and Retrieval
Text search / Information retrieval
Literature search and text mining
Finding synonyms (BioThesaurus)
Information extraction (e.g., protein phosphorylation sites)
Find the sequence for the rabbit alpha crystallin A chain
Find all alpha crystallin A chain classified in protein families
Search crystallins that have active enzyme activities
Find crystallins that have determined 3D structures
Database contents (reports)
Sequence & genomics databases (UniProt)
Protein family databases (PIRSF)
Database of protein functions (KEGG)
Databases of protein structures (PDB)
Proteomics databases (Swiss-2D)

4. Entrez Text Searches (http://www.ncbi.nlm.nih.gov/Entrez/)
Integrated one-stop search (

5. PubMed Literature Database(
Literature mining
PMID:

6. iProLINK: Protein Literature Mining Resource
RLIMS-P:
Text mining for protein phosphorylation
BioThesaurus:
Gene/protein name thesaurus: synonyms, ambiguous names…

7. BioThesaurus: Gene/protein name searches - synonyms, ambiguous names…
CRYAA
crystallin, alpha A
CRYA1
HSPB4…

8. RLIMS-P: Text mining for protein phosphorylation

9. PIR Text Search (I) (
Google type search vs.
Boolean searches: AND, OR, NOT

10. PIR Text Search (II)
Search: alpha crystallin A chain that are in protein families?
null = absent; not null = present
Search for synonyms

11. Argininosuccinate lyase (EC 4.3.2.1)
PIR Text Search (III)
Search: what crystallins are enzymes and what families they belong to?
Can you find which crystallins have 3D structure determined?
Argininosuccinate lyase (EC )

12. UniProt Text Search http://www.uniprot.org/
Find proteins related to diabetes and with 3D-structure determined?

13. Search continues…

14. Entry View: Sequence & Annotation
UniProt Report (I)
Sections of the record
Entry View: Sequence & Annotation

15. UniProt Report (II) – sequence and features

16. PIRSF: Full Length Classification iProClass Family Report(

17. KEGG Metabolic & Regulatory Pathways
KEGG is a suite of databases and associated software, integrating our current knowledge
on molecular interaction networks, the information of genes and proteins, and of chemical
compounds and reactions. ( (

18. PDB: Experimental 3D Structure Repository
Rat gamma-crystallin (chain A, B.)
Can you do a text search at PIR to find this (CRGE_RAT)? (

19. 2D-Gel Image Databases (http://us.expasy.org/swiss-2dpage/ac=P02489)(
Part of WORLD-2DPAGE: index to 2-D PAGE databases and services (