This book covers computational modeling of "biomolecular site dynamics". It also describes the use of rule-based modeling, in coordination with quantitative experimental approaches, to gain insights into site dynamics and to introduce the basic concepts and techniques of rule-based modeling. The book is divided into three parts. The first part covers the biological significance and physical chemistry of site dynamics. The second part provides an introduction to the essential methodology of rule-based modeling. The third part consists of examples of rule-based modeling capabilities.
INTRODUCTION. The biological and physicochemical foundations of biomolecular site dynamics. Motivation and background. Qualitative aspects of biomolecular interaction networks. Quantitative aspects of protein site dynamics. Quantitative aspects of protein site dynamics. Essential methodology. Overview of methods for specifying, visualizing and annotating models. Simulation techniques for non-spatial modeling. A survey of simulation techniques for spatial modeling. Methods for analyzing models. Example uses of rule-based modeling techniques. Multisite phosphorylation. Aggregation and self assembly. Allosteric regulation. Gene regulation. Isotopomer dynamics.