1. Overview of Enzyme, Protein and Network Databases
Cameron Wellock
Keck Graduate Institute

2. Protein Databases Types of Data Sequence Function Recognized Domains
Structural Information & Models
Pathway Information & Models

3. All-Purpose Databases

4. Entrez-Protein Part of a much larger library Provided through the NIH
Entrez provides Web and programmatic access
Search for coronavirus, and porcine… see what you get

5. PIR Protein Information Resource Arguably the most comprehensive

6. Swiss-Prot & TrEMBL A little bit of everything
Swiss-Prot carefully annotated
TrEMBL automatically annotated
Also PROSITE, ENZYME

7. BRENDA
Comprehensive Enzyme Database

8. Structure Databases

9. PDB Protein Data Bank Contains 3D models of proteins See also PDBSum
Show a model here! Using SPDBV

10. Entrez Structure Another part of Entrez library

11. Structural Classification DBs

12. COG Clusters of Orthologous Groups 3307 clusters at this time
Based on interspecies comparisons and sequence similarity

13. SCOP Structural Classification of Proteins Organized in a hierarchy
Based on secondary structure similarities

14. CATH Class, Architecture, Topology, Homologous Superfamily

15. Functional Classification Databases

16. ENZYME Nomenclature database Hierarchical organization

17. KEGG Kyoto Encyclopedia of Genes and Genomes
Its own classification scheme (KO)
Massive pathway maps
Links into COGS and ENZYME
Has a SOAP-based programmatic interface

18. Domain Databases

19. InterPro A large aggregated database, uses many sources in its search
* Do the SARS Demo

20. PROSITE
Also part of ExPASy

21. Special-Purpose Databases

22. HPRD
Human Protein Reference Database

23. Commercial Databases
Incyte BioKnowledge (

24. Places to Look http://bmbsgi10.leeds.ac.uk/moldb.html