Proteins as Netwoks: Usefulness of Graph Theory in Protein Science
Alessandro Giuliani, Luisa Di Paola, Paola Paci, Micol De Ruvo, Caterina Arcangeli, Daniele Santoni and Massimo Celino
Chapter DOI: 10.2174/9781608054879113010011
The consideration of protein molecules as graphs whose nodes and edges are
respectively the aminoacid residues and the non covalent contacts between them permits
to develop very effective models of protein behavior. The network paradigm not only
allows for a drastic reduction of the amount of information needed to represent a protein
3D structure, but provides a set of quantitative descriptors derived from mathematical
graph theory endowed with crucial information as for protein biological role. Here we
will briefly comment about the relevance of graph descriptors in registering the relevant
features of the molecular dynamics of solvation process and sketch the possibility to
consider contact map as the ‘macromolecular’ analogue of small organic molecules
Protein contact maps, systems biology, chemo-informatics,
computational biology, molecular dynamics.
Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.