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SCOP – Protein structure classification CATH – Protein structure classification

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. SCOP: S tructural C lassification o f P roteins.

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SCOP – Protein structure classification CATH – Protein structure classification

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  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 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

  3. Node Parents of node Children of node

  4. Node Parents of node Children of node

  5. CATH:Protein Structure Classificationby Class, Architecture, Topology and Homology http://www.cathdb.info/latest/index.html • 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

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

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

  8. GenTHREADER Output

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

  10. SWISS-MODEL An automated protein modeling server. http://swissmodel.expasy.org/

  11. 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.

  12. SWISS-MODEL Get PDB file by E-mail Load to J-Mol

  13. Homology Modeling Single Structure

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

  15. 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)

  16. ModBaseA Homology Model Database

  17. Ligand Binding Site

  18. 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

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