Proteins as Netwoks: Usefulness of Graph Theory in Protein Science

Pp. 309-317 (9)

Alessandro Giuliani, Luisa Di Paola, Paola Paci, Micol De Ruvo, Caterina Arcangeli, Daniele Santoni and Massimo Celino

Abstract

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 structural formula.

Keywords:

Protein contact maps, systems biology, chemo-informatics, computational biology, molecular dynamics.

Affiliation:

Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.