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• PDB - Protein Data Bank• 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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PDB fileAccession number
Java based visualization tools
Structural Classification
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PDB provides the atomic coordinates of the structure :
Which can be viewed by different visualization tools
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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
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
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Ligand Binding Site
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Excersize The sequence below belongs to the Prion that causes the “mad cow” disease. This protein becomes toxic
when it gets into the brain and misfolds causing native cellular prions to deform and aggregate. In structural terms, the prion toxicity in leaded by a folding change into an instable structure.
>PRION_1ag2
GLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY
Use PSIpred, geneTHREADER and PROFsec in order to predict its secondary and tertiary structures. Based on the secondary and tertiary structure predictions
1. Can you suggest the region which could be responsible for the structural instability?
2. What is the secondary structure in the real solved structure?
3. What is the expected structural change in this region?
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PSIPRED
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geneTHREADER
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PROFsec
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PROFsec
Answer : alpha helix geneTHREADER turn into B-sheet PSIPRED anf PROFsec, prediction in this area are not consistent in the different tools.