SOLVED: Take a protein structure from Protein Data Bank (PDB). Calculate the protein structure as a reduced chain (virtual bond model) where each residue is represented by its alpha carbon (C) and side chain centroids (S). The successive alpha carbons are connected by virtual bonds. L1, L0, and L1 refer to the bond length between residue 1 and residue 1 1, the bond angle between the bond vectors i and i-1, and the torsional (rotational dihedral) angle defined by the bond vectors i 1, i, and i-1.
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The Protein Data Bank (PDB) contains more than 150,000 different three-dimensional biomolecular structures obtained by x-ray crystallography, NMR, and cryo-EM. Each protein structure deposited into the database is given a PDB ID. Several PDB IDs represent proteins whose structures resemble letters from the Roman alphabet. Find each protein structure in the PDB and view the three-dimensional structure using JSmol, PYMOL, or a similar structure viewer. PDB IDs: 2QYC, 2BNH, 2Q5R, 1XU9, 3H7X, 1OU5,
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