ANSWER WITH MATLAB CODE

The B-factor of atoms in protein structures deposited in the PDB database (www.pdb.org) describes the displacement of each atom from its average location. The atoms on the surface of proteins tend to be more mobile and as a result have large B-factor values, whereas those in the core of the protein are restricted and have smaller B-factor values. Write a function pdb_bfactor that takes a four letter PDB identifier and returns the average B factor of all of the CA (alpha carbon) atoms. Your function should download the pdb file from pdb.org website, e.g., if the PDB id "1crn" is given as input, your function should download the protein file from https://www.rcsb.org/pdb/files/1crn.pdb . You can use the websave() function to write the contents of a webpage into a file. Note that each of the PDB ATOM entry lines is formatted such that the characters 13-16, 31-38, 39-46, 47-54, and 61-66 contain the atom type (e.g., "CA", ignoring any spaces), the x,y,z coordinates, and the B-factor of an atom, respectively. You only need to consider the lines that start with the word "ATOM" and have the atom type "CA". A suggested outline of the steps you would follow in pdb_factor is given below.

Let X be the input PDB identifier (e.g., having value "1crn").

Using the websave() function, download the pdb file from the web and save it to X.pdb file. Use string concatenation to construct the filename (You need to put together the value of X and the file extension '.pdb').

Open the X.pdb file for reading using fopen().

Read the file line by line, using a while loop.

If a line begins with "ATOM" and has "CA" as the atom type, add its b-factor to a vector named bfactors.

After the while loop processes all of the lines, close the file using fclose().

Return the average of the bfactors as output argument.

THE CORRECT ANSWER WILL RETURN THE FOLLOWING OUTPUT EXACTLY:

>> pdb_bfactor('1ubq') ans = 10.5837