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Description and classification of protein structures
Mathematical Biology| Speaker: | Peter Røgen, Department of Mathematics, Technical University of Denmark |
| Location: | 3106 MSB |
| Start time: | Mon, Apr 30 2007, 4:10PM |
Description
Proteins are long chain molecules that fold into
beautiful and complicated structures
before fulfilling their functions in the living organisms. This talk focus on some mathematical
attempts to bring classification of protein
native structures from relative comparison to
known examples to absolute description of each structure - one step up the scientific
evolutionary ladder.
In the talk, I will shortly introduce some of
the reduced mathematical representations of
protein backbones and say a few words on
similarity measures on the space of protein
structures. The main focus of the talk will be
on structural descriptors and on how to use
structural descriptors to give the best possible
pseudo metric on the space of all known protein
folds. In the talk, I will introduce three
families of descriptors:
The generalized Gauss integrals, that are based
on the writhe of an open space curve and come
from integral formulas of the Vassiliev knot
invariants.
The average crossing pattern occurrences,
that also generalize the writhe.
A new family based on a coloring of the protein
backbone and on the distance excess / parabolic
section of curves. This family is constructed to
be "orthogonal" to the writhe.