About

This project is designed to help in work with PDB files, which represent the three-dimensional structure of proteins. It allows to calculate some parameters of the protein structure: the geometric center, center of mass, gyration radius of domains, distance between domains. It is also possible to compare two structures by calculating the RMSD (root-mean-square deviation of atomic positions).

Scripts

calc_params.py:

Script calc_params.py is designed to calculate parameters of two specified domains in a structure. To run this script set parameters:

• structure_id --- id of structure
• pdb_filename --- filename to PDB structure
• d1_info --- domain 1 info (turple: chain_number, start_residue, finish_residue)
• d2_info --- domain 2 info (turple: chain_number, start_residue, finish_residue)

After running this script the geometric center, center of mass, gyration radius of domains, distance between domains will be calculated. Geometric center calculated as:

Mass center calculated as:

Gyration radius calculated as:

Where: N - number of atoms, m_i - mass of i atom, r_i - coordinates of i atom.

Distance calculated as the Euclidean distance between coordinates of mass centers of domains.

compare_domains.py:

Script compare_domains.py is designed to compare the two structures by calculating the RMSD (root-mean-square deviation of atomic positions). To run this script set parameters:

• structure1_id, structure2_id --- id of structure
• s1_filename, s2_filename --- filename to PDB structure
• d1_info, d2_info --- domain info (turple: chain_number, start_residue, finish_residue)

After running this script the gyration radius of domains and the RMSD will be calculated. RMSD calculation is implemented using the set_atoms function from the Biopython library.

Example 1

To test scripts you can run it for modeled structure of nanobody 2Rs15d-GGGS-2Rs15d where 2Rs15d is sequences of VHH antibody Camelus dromedarius, GGGS - linker. Coordinates of first subunit is 1-115 residues, coordinates of second subunit is 120-234 residues.

calc_params.py configuration:

# configuration
structure_id = "test"
pdb_filename = "test_data/2Rs15d-link-2Rs15d.pdb"
d1_info = (0, 1, 115)
d2_info = (0, 120, 234)

compare_domains.py configuration:

# configuration
structure1_id = "test"
s1_filename = "test_data/2Rs15d-link-2Rs15d.pdb"
d1_info = (0, 1, 115)

structure2_id = "test"
s2_filename = "test_data/2Rs15d-link-2Rs15d.pdb"
d2_info = (0, 120, 234)

Example 2

There is real structure of VHH 2Rs15d in protein data bank (B chain of HER2-Nb complex 5my6). This structure was download and saved in 5my6.ent file. You can compare crystal structure of 2Rs15d (1 chain, 1-115 residues of 5my6 complex) with modeled structure 2Rs15d (0 chain, 1-115 or 120-234 residues of 2Rs15d-GGGS-2Rs15d model) by using compare_domains.py script.

compare_domains.py configuration:

# configuration
structure1_id = "modeled"
s1_filename = "test_data/2Rs15d-link-2Rs15d.pdb"
d1_info = (0, 1, 115)

structure2_id = "crystal_structure"
s2_filename = "test_data/5my6.ent"
d2_info = (1, 1, 115)