Task Structural Alignments

In order to evaluate the similarity between protein structures, the structures have to be superimposed in 3D. A multitude of methods are available to achieve this task. Also, there are many different measures to quantify structural similarity. In this task we will explore different methods and compare different measures to get a feeling for the structural similarity they imply. We will then apply structural alignment to evaluate some sequence-based alignments generated in Task 2 (Run sequence searches on the disease gene product and produce alignments).

Theoretical background talk

The introductory talks should given an overview of

• short review of SCOP und CATH
• Alignment methods:
  • the one used by CATH (CATHEDRAL)
  • Topmatch
  • SAP or CE
  • LGA (see http://proteinmodel.org/AS2TS/LGA/lga_format.html for documentation)
• Modelling scores:
  • RMSD
  • Topmatch scores
  • GDT
  • LCS