Structure analysis and homology modeling
We use several example to learn the general steps for protein modeling.
- Display the structure of pig insulin
find out the hydrophobic residues between the surface of dimer interaction.
- Display the structure of sperm whale myoglbin
and compare the difference of the alpha helices.
- Display the structire of mouse immunoglobulin
and find out the disulphide bridges between the two heavy chains, the heavy
and light chain, and within each domian.
- Display the structire of Xenopus nucleosome
and find the DNA helix and 8 protein subunits. Show the histone tail and the
- Display the structire of green fluorescent proteins
Find the Ser65-Tyr66-Gly67 residues and the CRO66 residue which is the source
of the light.
- Compare the differences of the heme group of human hemoglobin alpha
subunit in deoxy
- Compare the N-terminal domain of human cacinoembryonic antigen
and the variable domain of human immunoglobulin light chain
make superimposition with three residue pairs (C22-V21, W37-W33, C83-L88)
- Compare the structure of pokeweed antifungal peptide
and spider toxin
and measure the Ca-Ca distance and dihedral angles of three
disulfide bonds for each molecule, make superimposition based on three
- Make analysis of rat metallothionein structure
and human metallothonein alpha
domain, measure the distances of the metal-Cys clusters of both domains
- Predict the three-dimensional structure of the second domain
of the human carcinoembryonic antigen
using SwissModel and Phyre2, analize the results.
- Predict the three-dimensional structure of the inner membrane protein of