modeling

We use several example to learn the general steps for protein modeling.

Display the structure of pig insulin 4INS find out the hydrophobic residues between the surface of dimer interaction.
Display the structure of sperm whale myoglbin 1MBN and compare the difference of the alpha helices.
Display the structire of mouse immunoglobulin 1IGT 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 1AOI and find the DNA helix and 8 protein subunits. Show the histone tail and the lysine resdues.
Display the structire of green fluorescent proteins 1GFL, 1KYS, 1EMA 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 2HHB and oxy 1HHO form.
Compare the N-terminal domain of human cacinoembryonic antigen 2QSQ and the variable domain of human immunoglobulin light chain 7FAB make superimposition with three residue pairs (C22-V21, W37-W33, C83-L88)
Compare the structure of pokeweed antifungal peptide 1DKC and spider toxin 1QK6 and measure the Ca-Ca distance and dihedral angles of three disulfide bonds for each molecule, make superimposition based on three disulfide bonds
Make analysis of rat metallothionein structure 4MT2 and human metallothonein alpha 1MHU and beta 2MHU 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 CEA21_HUMAN using Phyre2, analize the results.
Predict the three-dimensional structure of all seven domains of the human carcinoembryonic antigen CEAM5_HUMAN_All using Phyre2, analize the results.
Predict the three-dimensional structure of Leptin
Predict the three-dimensional structure of the inner membrane protein of Pisum sativam PPF1_PEA using the Intensive mode under Phyre2.

Applied Bioinformatics Course [中文]