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• 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
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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
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Parents of node
Childrenof node
Node
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Parents of node
Childrenof node
Node
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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
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CATH: Protein Structure Classificationby Class, Architecture, Topology and Homology
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genTHREADER
Input sequence
Type of Analysis(PSIPRED,MEMSAT,
genTHREAD)
http://bioinf.cs.ucl.ac.uk/psipred/psiform.html
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GenTHREADEROutput
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GenTHREADEROutput
The output sequences show some extent of sequence homologyBut high level of secondary structure conservation
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SWISS-MODEL
An automated protein modeling server.
http://swissmodel.expasy.org/
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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.
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SWISS-MODEL
Get PDB file by E-mail
Load to J-Mol
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Single StructureHomology Modeling
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Swiss-Model file
Structures used for the homology
model
query
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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)
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ModBaseA Homology Model Database
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Ligand Binding Site