Despite the promises made that genomic sequencing would transform therapy by introducing a new era of personalized medicine, relatively few tangible breakthroughs have been made. This has led to the recognition that complex interactions at multiple spatial, temporal, and organizational levels may often combine to produce disease. Understanding this complexity requires that existing and future models are used and interpreted within a framework that incorporates knowledge derived from investigations at multiple levels of biological function. It also requires a computational infrastructure capable of dealing with the vast quantities of data generated by genomic approaches. In this review, we discuss the use of molecular modeling to generate quantitative and qualitative insights at the smallest scales of the systems biology hierarchy, how it can play an important role in the development of a systems understanding of disease and in the application of such knowledge to help discover new therapies and target existing ones on a personal level. WIREs Syst Biol Med 2012, 4:585–598. doi: 10.1002/wsbm.1186

This article is categorized under:

• Biological Mechanisms > Chemical Biology
• Analytical and Computational Methods > Computational Methods
• Models of Systems Properties and Processes > Mechanistic Models
• Translational, Genomic, and Systems Medicine > Translational Medicine