Visualization of protein domain interaction interfaces

Abstract

Visualization of protein domain interaction interfaces is useful in analyzing the chemical and geometrical nature of protein domain-domain interactions. This thesis explains the method to visualize the protein domain-domain interaction interfaces and introduces two programs: InterFacer and PDIIIDB. InterFacer is a molecular viewer specialized to visualize protein domain-domain interfaces. PDIIIDB is a database of images of protein domain-domain interaction interfaces. Both programs use hierarchical protein domain structure classification information with a real-time interface definition algorithm. They provide information for analyzing the chemical and geometrical nature of protein domain-domain interactions. InterFacer helps user to visualize a protein domain-domain interaction interface and analyze the property of the interface interactively. PDIIIDB supports comparative visualization of interfaces between same families.