Just something I did for leisure :) .You need to download PDB viewer, Yasara/Accelerys for a clear understanding of this subject.

1. by
Elda Nurafnie binti Ibnu Rasid

2.  Able to define Homology modeling
 Understand the basic steps of Homology
modeling

3.  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 protein
 To predict protein structure based on known 3D
shape protein as the template

4. TEMPLATE
?
UNKNOWN STRUCTURE
SEQUENCE ALIGNMENT
STRUCTURAL MODEL
STRUCTURAL MODEL

6. 1. To look for homologous protein
2. To search for template

7. 1
2
3
http://blast.ncbi.nlm.nih.gov/

10. http://www.ebi.ac.uk/Tools/msa/clustalw2/
1
2

12.  CPHmodel
 EsyPred3D
 SWISS-MODEL

13. http://swissmodel.expasy.org/

14.  Swiss-PdbViewer 4.1
 YASARA
 Accelrys DS Viewer 5.0

15. PDB Viewer

16. YASARA

17.  Verification of Model
 Verify3D
 Errat Plot
 Ramachandran Plot

18.  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/