Graph Construction for Modeling Protein 3D Structures: Consequences and Improvements

• Activity Number: 129
• Type: Contributed
• Date/Time: Monday, July 30, 2012 : 8:30 AM to 10:20 AM
• Sponsor: Biometrics Section
• Author(s): Amy Wagaman*+
• Companies: Amherst College
• Keywords: Networks ; Proteins ; Small-world ; Graph theory ; Random graph generation

Abstract

Researchers often model folded protein 3D structures as graphs with amino acids as the vertices and edges representing contacts between amino acids. Many possible constructions exist based on whether the graph is made using all atoms or only C-alpha atoms or only C-beta atoms, deciding what counts as contacting for determining the graph edges, and deciding to ignore or not ignore trivial contacts from amino acids close in the protein sequence. However, there is no consensus about what construction to use or what the major issues are with each construction in the literature. We investigate different constructions and examine their effect on various graph measures. We also consider the "small-world" network model for proteins, discuss its validity under the different constructions, and discuss random protein graph generation.