Aims

• To reinforce the concepts of three-dimensional transformations in the context of structure alignment.
• To revise some of the concepts in protein structure alignment.

Objectives

After this practical you will:

• be aware of how the transformation and fitting code seen in earlier lectures and practicals can be used in structure alignment.

Exercises

1. In DALI:

   "An internal coordinate frame is defined by an ordered pair of SSEs (centering one SSE at the origin, aligning it with the y axis, and rotating the molecule around this axis so that the center of a second SSE is in the positive x-y plane)."
   From "Mapping the Protein Universe" by Liisa Holm and Chris Sander (Science, vol. 273, 595-602, 1996)

   Suppose that points P1n and P1c are, respectively, points at the N and C ends of a line segment representing secondary structure element S1, and that points P2n and P2c are, respectively, points at the N and C ends of a line segment representing secondary structure element S2. Describe the steps needed to transform this pair of SSEs to the internal coordinate frame.

2. A method for bringing two residues into the same frame of reference is described in the first paragraph of section 2(e) of: Taylor W.R. and Orengo C.A. (1989) "Protein structure alignment", J. Mol. Biol., 208, 1-22 (PubMed).

   1. Describe how this can be achieved using the functions in the transformation and grometry libraries.

   2. Suggest an alternative way to bring two residues into the same frame of rerference.