• 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-Protein Data Bank SCOP –Protein structure classification CATH –Protein structure classification genTHREADER–3D structure prediction Swiss-Model–3D.
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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
PDB fileAccession number
Java based visualization tools
Structural Classification
PDB provides the atomic coordinates of the structure :
Which can be viewed by different visualization tools
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
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.
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?
PSIPRED
geneTHREADER
PROFsec
PROFsec
Answer : alpha helix geneTHREADER turn into B-sheet PSIPRED anf PROFsec, prediction in this area are not consistent in the different tools.