Numerical analysis of binding data: advantages, practical aspects, and implications.

Publisher Summary This chapter focuses on some important aspects of the application of a numerical methodology for the binding question. The advantages of the numerical method over analytical methods are discussed in the chapter. The chapter provides an overview of the numerical methodology utilized within BIOEQS (a computer program) for solving complicated binding equilibria. The chapter illustrates the way an example system is treated using a numerical solver. Typical binding data is simulated for the model presented in the chapter, and a demonstration of the fit and output are given. The chapter explores the information content of multidimensional binding data and discusses the unique recovery of the free energy values in complex systems. In addition to expanding the scope of the models, which can be examined, moving to a numerical method of calculating binding profiles presents the advantage of generalizing the problem under consideration. The development of a computer program (BIOEQS) for the analysis of ligand binding and subunit assembly data for macromolecular complexes is described in the chapter. The data analysis program, BIOEQS, has been designed for the simultaneous analysis of multiple binding data sets. By employing BIOEQS as a tool, scientists can concentrate more time on model testing and experimental design, as opposed to confronting both the drudgery and constraints of developing and applying analytical expressions to describe data.