scop –protein structure classification cath –protein structure classification genthreader–3d...

• SCOP – Protein structure classification • CATH – Protein structure classification • genTHREADER – 3D structure prediction• Swiss-Model – 3D structure prediction• ModBase - A database of 3D struc.

Predict.

Protein Structure Prediction II

SCOP: Structural Classification of Proteins

http://scop.mrc-lmb.cam.ac.uk/scop/

•Based on known protein structures

•Manually created by visual inspection

•Hierarchical database structure:–Class, Fold, Superfamily, Family, Protein

and Species

Parents of node

Childrenof node

Node

Parents of node

Childrenof node

Node

CATH: Protein Structure Classificationby Class, Architecture, Topology and Homology

http://www.cathdb.info/

•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

CATH: Protein Structure Classificationby Class, Architecture, Topology and Homology

genTHREADER

Input sequence

Type of Analysis(PSIPRED,MEMSAT,

genTHREAD)

http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

GenTHREADEROutput

GenTHREADEROutput

The output sequences show some extent of sequence homologyBut high level of secondary structure conservation

SWISS-MODEL

An automated protein modeling server.

http://swissmodel.expasy.org/

SWISS-MODEL• The SWISS-MODEL algorithm can be divided into

three steps:

1.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.

2.Check sequence identity with target: All templates

with sequence identities above 25% are selected

3.Create the model using the ProModII program. You

get this as a SwissModel-Model file.

SWISS-MODEL

Get PDB file by E-mail

Load to J-Mol

Single StructureHomology Modeling

Swiss-Model file

Structures used for the homology

model

query

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)

ModBaseA Homology Model Database

Ligand Binding Site