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The topic of a student research:

Patterns recognition of Supersecondary structures

Abstract
The goal of this project to prove the hypothesis that proteins with
identical supersecondary structure have common sequence patterns even if
they belong to different protein families and have very low sequence
similarities. For beta sandwich proteins, which are the focus of the
current research, proteins with the same supersecondary structure have an
equal number of strands in a domain and the same hydrogen bond contacts
arrangement of the strands in two beta sheets. However, these proteins
may strongly differ in a number and composition of residues in strands,
and in lengths and conformations of loops between the strands.
Application of usually used methods of sequence alignment to find the
conserved positions is not available here because of very low sequence
similarity (less than 10%). To find common sequence regularities for
these proteins a new procedure of multiple sequence alignment was
developed. It is based on the alignment of residues that form hydrogen
bond contacts between strands. The aim of a student is: 1) to test this
algorithm for different protein families; 2) to find positions conserved
for a given family; 3) to test a set of residues at the conserved
positions as pattern recognition.