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Comprehensive Overview of Protein Structure Prediction and Classification Techniques

This document provides an in-depth analysis of protein structure prediction methods and classification systems. It covers tools such as SCOP, CATH, genTHREADER, Swiss-Model, and ModBase, detailing their hierarchical structures and functionalities. Key aspects like secondary structure composition, overall domain shape, and evolutionary conservation are discussed. The automated processes involving template searching, sequence identity checks, and model generation are highlighted, emphasizing the significance of homology modeling in achieving accurate protein structures.

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Comprehensive Overview of Protein Structure Prediction and Classification Techniques

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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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