In this exercise, we will model the structure of a protein's 1D sequence using one of its homologs as a template. We will then compare the generated homology model to the actual structure of the protein to gain insight.
Your Protein Sequence | Your Template PDB |
MG3368B_protein1 | |
GE1527P_protein2 | |
RK10653A_protein3 | |
MH7542A_protein4 | |
PX15502A_protein5 |
Your Protein Model | PDB code | Chain |
The Ligand Binding Domain Of The Vitamin D Nuclear Receptor | 2hcd | A |
Shikimate Kinase From Mycobacterium Tuberculosis | 2dft | C |
The Pleckstrin Homology Domain Of Akt1 In Cancer (Akt1-Ph_e17k) | 1p6s | A |
Avian Respiratory Complex Ii | 1nek | B |
Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase | 1cyg | Since this protein only has one chain, leave this field blank in FATCAT. |
Your Protein Model | Download Actual Structure files | Chain |
model_protein1 | MG3368B_protein1.pdb | A |
model_protein2 | GE1527P_protein2.pdb | A |
model_protein3 | RK10653A_protein3.pdb | A |
model_protein4 | MH7542A_protein4.pdb | A |
model_protein5 | PX15502A_protein5.pdb | A |
There are many other programs and websites for modeling. You can also try advanced modeling tools available from The Joint Center for Molecular Modeling (JCMM) - Server Links
There are some more links in the Review of the Steps in Comparative Modeling.