Shibberu Laboratory
Research
Scoring Aligned Protein Folds
Proteins play a key role in nearly all of the biochemical processes of
living organisms. Identifying the biological function of individual
proteins is an important and challenging problem. The geometry of a
protein's fold largely determines the protein's specific biological
function. A better understanding of nature's protein fold space will
lead to major advances in biology and will ultimately make it possible
to design new proteins with novel functions.
Nature's protein fold space is the result of many years of evolution.
We can study the evolution of proteins by making comparisons - either
by comparing protein sequences or by comparing protein folds.
Fold-based comparisons are much more informative and robust. However,
the best way to aligning protein folds is not well understood
mathematically or even biologically. In this IRCBC research project, we
investigate the simpler problem of how best to score protein folds
which have already been aligned manually by human experts. To keep the
problem tractable, we will restrict ourselves to the fold space of a
particular protein family, e.g.,
the globin protein family.
This research project will require familiarity with molecular biology
or biochemistry and a background in linear algebra and statistics.
Although bioinformatics software tools will be used, a limited amount
of programming may be necessary.
