Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis.

ABSTRACT: Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents 'Domain expansion' for proteins and RNAs, 'Virtual reaction and nodes' that are responsible for illustrating domain-based interaction and 'InnerLink' that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork,

SUBMITTER: Kurata H 

PROVIDER: S-EPMC2175333 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature