Protein Structure Prediction II

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Presentation transcript:

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: 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

Node Parents of node Children of node

Node Parents of node Children of node

CATH: Protein Structure Classification by 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

CATH: Protein Structure Classification by Class, Architecture, Topology and Homology

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

GenTHREADER Output

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

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

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.

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

Homology Modeling Single Structure

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

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)

ModBase A Homology Model Database

Ligand Binding Site

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