modeling

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

Display the structure of sperm whale myoglbin (1MBN) with online molecular display tools (Cn3D, JMol, WebMol, Jean-Lib, Swiss PDBViewer), compare the difference of the alpha helices
Compare the differences of the heme group of human hemoglobin alpha subunit in deoxy (2HHB) and oxy (1HHO) form
Display human (1HZH) and mouse (1IGT) immunoglobulin molecule with Cn3D, compare the overall structure and the differences
Compare the N-terminal domain of human cacinoembryonic antigen type 1 (2GK2) and type 5 (1QSQ) with Swiss PDBViewer, calculate the RMSD of C-alpha superimposition
Compare the N-terminal domain of human cacinoembryonic antigen (1QSQ) and the variable domain of human immunoglobulin light chain (7FAB) with Swiss PDBViewer, make superimposition with three residue pairs (C22-V21, W37-W33, C83-L88)
Compare the structure of pokeweed antifungal peptide (1DKC) and spider toxin (1QK6), 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
Make analysis of pig insulin structure (4INS), find out the hydrophobic residues between the surface of dimer interaction
Make analysis of bovine trypsin and inhibitor complex, find out the residues involving in chemical reaction

Predict the three-dimensional structure of the second and third domain (two IgG constant domains) of the human carcinoembryonic antigen (CEAM5_HUMAN) using SwissModel and 3D-Jigsaw, compare the results
Predict the three-dimensional structure of Pseudomonas pseudoalcaligenes Organophosphorus hydrolase (Q5W503_PSEPS), compare the results with it's template 1P9E

Applied Bioinformatics Course