HOMOLOGY MODELING

by

Elda Nurafnie binti Ibnu Rasid

LEARNING OUTCOME

Able to define Homology modeling Understand the basic steps of Homology

modeling

WHAT IS HOMOLOGY MODELING? Homologous proteins

Portion of 2 proteins with similar amino acids : Conserved Region

Highly similar proteins may have same basic function

Homology Modeling Comparative modeling of proteinTo predict protein structure based on known

3D shape protein as the template

HOMOLOGY MODELING CONCEPT TEMPLATE

?UNKNOWN STRUCTURE

SEQUENCE ALIGNMENT

STRUCTURAL MODEL

STRUCTURAL MODEL

BASIC STEPSDatabase Searching for homologous proteins

Amino acids alignment

Model Building

Model Refinement and Evaluation

DATABASE SEARCHING

1. To look for homologous protein2. To search for template

DATABASE SEARCHING :BLAST

1

2

3

http://blast.ncbi.nlm.nih.gov/

DATABASE SEARCHING :BLAST RESULT

DATABASE SEARCHING :SEARCH FOR SEQUENCE

AMINO ACID ALIGNMENT: CLUSTALW2 http://www.ebi.ac.uk/Tools/msa/

clustalw2/

1

2

AMINO ACID ALIGNMENT: RESULT CLUSTALW2

MODEL BUILDING CPHmodel EsyPred3D SWISS-MODEL

MODEL BUILDING http://swissmodel.expasy.org/

STRUCTURE VIEWER

Swiss-PdbViewer 4.1 YASARA Accelrys DS Viewer 5.0

MODEL BUILDING :RESULTPREDICTED UNKNOWN PROTEIN STRUCTURE (CGTASE)

PDB Viewer

MODEL BUILDING :RESULTPREDICTED UNKNOWN PROTEIN STRUCTURE (CGTASE)

YASARA

MODEL REFINEMENT AND EVALUATION Verification of Model

Verify3DErrat Plot Ramachandran Plot

REFERENCES http://blast.ncbi.nlm.nih.gov/ http://www.ebi.ac.uk/Tools/msa/clustalw2/ http://www.yasara.org/ http://spdbv.vital-it.ch/download.html http://swissmodel.expasy.org/ http://nihserver.mbi.ucla.edu/ERRATv2/ http://nihserver.mbi.ucla.edu/Verify_3D/