Structural Bioinformatics
Assignment 2
The objective of this assignment is to familiarize you with the PDB data
format. To successfully fulfill the assignment, follow the
instructions below, and send the resulting file to my email
avraham.samson@biu.ac.il
with the words "Structural Bioinformatics" in the title.
Other questions, should be answered in the body of the e-mail.
Question 1. Sometimes, you will need to select the coordinates of one
structure only. In this exercise you will select and save part of
the PDB file only.
-Download 2KZ1 (Interferon in complex with the receptor) from the PDB
-Open it in pymol or any other molecular viewer of your choice.
-Remove all hydrogen atoms (i.e. TYPE "select hydro" and then "remove sele" OR click A-->Hydrogens-->Remove)
-There are 10 models in the structure, click on the lower right triangle to see them. To split the models type "split_states 2kz1".
-Select chain A of model no. 2. (i.e. click Mouse-->Selection Mode-->Chains)
-Save selected chain into PDB file and send by email.
There is another way to do this, namely to open the PDB file in Windows wordpad or Notepad and edit out unwanted text.
Question 2. Write a SMILES code of aspirin (acetylsalicylic acid). Note, there
are many solutions to this problem. Here is one solution:
OC(=O)C1=C(C=CC=C1)OC(=O)C
Please send me another one.
Question 3. Describe in 2-3 sentences, a new way to represent structure in a compact way (not by removing hydrogens or SMILES).