Practical 3

Main chain tracing

Aims

• To give practice in reading and summarising a research article.

Objectives

After this practical you will be able to:

• describe bioinformatics problems and computational approaches to solving them;
• summarise problems and methods described in research articles

Exercise

In this exercise you will summarise the problem and computational solution that are described in:

• R. J. Morris, A. Perrakis and V. S. Lamzin (2002) ARP/wARP's model-building algorithms. I. The main chain. Acta Cryst., D58, 968-974. doi:10.1107/S0907444902005462

In part (a) you will implement a program that performs a simplified main chain tracing task. In part (b) you will compare and contrast part (a) with the more challenging problem and more sophisticated solution in the work of Morris et al. (2002).

• File p3.pdb contains the coordinates of a set of alpha-carbon atoms, but these are not given in the order in which they occur in a protein chain. That is, the residue sequence numbers do not correspond to the actual ordering of the residues in the protein chain.

  Write a program that identifies the order of these residues in a protein chain. Remember that the separation between two consecutive alpha-carbon atoms in a protein chain is about 3.8 Å.

• Write a report that summarises the problems and methods described in the paper by Morris et al. (2002).

  After reading your report the reader should:

  • understand the computational problem that is being addressed in the paper, and how this differs from the problem in part (a);
  • understand what needs to be done to implement a solution to the problem, and how this differs from the solution to part (a).

  You can make the following assumptions about the reader:

  • the reader's knowledge and background in computing science is similar to your own;
  • the reader is aware that proteins consist of chains of amino acid residues, and that each amino acid residue has a central carbon atom called the alpha-carbon.

  You should use a clear and straightforward writing style.

What to submit

• Your program and the result of running the program with data file p3.pdb (output.txt). File output.txt should consist of a list of residue sequence numbers (one per line) in the order in which the residues in file p3.pdb occur in the protein chain. For example, if you have the input file:

  ATOM      1  CA  ALA A   1      -8.333   3.374   4.249
  ATOM      2  CA  ALA A   2      -7.884   3.968  -1.519
  ATOM      3  CA  ALA A   3      -4.783   2.702   0.280
  ATOM      4  CA  ALA A   4      -4.779   4.558   3.598
  

  then the output could be:

  1
  4
  3
  2
  

• A PDF file.

You should submit your solution via the Fire system before 23:59 on Wednesday 2 December 2015.