1. Protein Structure Prediction II
SCOP – Protein structure classification
CATH – Protein structure classification
genTHREADER – 3D structure prediction
Swiss-Model – 3D structure prediction
ModBase - A database of 3D struc. Predict.

2. SCOP: Structural Classification of Proteins
Based on known protein structures
Manually created by visual inspection
Hierarchical database structure:
Class, Fold, Superfamily, Family, Protein and Species

4. Node
Parents of node
Children
of node

5. Node
Parents of node
Children
of node

9. CATH: Protein Structure Classification by Class, Architecture, Topology and Homology
Class: The secondary structure composition: mainly-alpha, mainly-beta and alpha-beta.
Architecture: The overall shape of the domain structure. Orientations of the secondary structures : e.g. barrel or 3-layer sandwich.
Topology: Structures are grouped into fold groups at this level depending on both the overall shape and connectivity of the secondary structures.
Homologous Superfamily: Evolutionary conserved structures

10. CATH: Protein Structure Classification by Class, Architecture, Topology and Homology

12. genTHREADER http://bioinf.cs.ucl.ac.uk/psipred/psiform.html
Input sequence
Type of Analysis
(PSIPRED,MEMSAT,
genTHREAD)

13. GenTHREADER
Output

14. GenTHREADER
Output
The output sequences show some extent of sequence homology
But high level of secondary structure conservation

15. An automated protein modeling server.
SWISS-MODEL
An automated protein modeling server.

16. SWISS-MODEL The SWISS-MODEL algorithm can be divided into three steps:
Search for suitable templates: the server finds all similarities of a query sequence to sequences of known structure. It uses the BLASTP2 program with the ExNRL-3D database (a derivative of PDB database, specified for SWISS-MODEL). You get these partial results as a SwissModel TraceLog file.
Check sequence identity with target: All templates with sequence identities above 25% are selected
Create the model using the ProModII program. You get this as a SwissModel-Model file.

17. SWISS-MODEL
Get PDB file by
Load to J-Mol

18. Homology Modeling
Single Structure

19. Structures used for the homology model
Swiss-Model file
query
Structures used for the homology model

20. Comparative Modeling
Accuracy of the comparative model is related to the sequence identity on which it is based
>50% sequence identity = high accuracy
30%-50% sequence identity= 90% modeled
<30% sequence identity =low accuracy (many errors)

21. ModBase A Homology Model Database

24. Ligand Binding Site

25. A Clan is defined as a group of Pfam families which share a common evolutionary origin.
They are generally different at the sequence and functional level but similar at the structure level.
Histone superfamily