The combination of faster, more advanced computers and more quantitatively oriented biomedical researchers has recently yielded new and more precise methods for the analysis of biomedical data. These better analyses have enhanced the conclusions that can be drawn from biomedical data, and they have changed the way that experiments are designed and performed. This volume, along with the 2 previous Computer Methods volumes for the Methods in Enzymology serial, aims to inform biomedical researchers about recent applications of modern data analysis and simulation methods as applied to biomedical research.

Key Features

* Presents step-by-step computer methods and discusses the techniques in detail to enable their implementation in solving a wide range of problems
* Informs biomedical researchers of the modern data analysis methods that have developed alongside computer hardware
*Presents methods at the "nuts and bolts" level to identify and resolve a problem and analyze what the results mean


Biochemists, molecular biologists, cell biologists, biomedical researchers, microbiologists, and developmental biologists

Table of Contents


Measurement and Analysis of Equilibrium Binding Titrations

1. Material Requirements for Binding Measurements

2. Monitoring a Binding Reaction

3. The Binding Equation and Its Relationship to Binding Measurements

4. Plotting and Analysis of Binding Data

5. Protein Concentration Is Important: Equilibrium Versus Stoichiometric Conditions

6. When Are Total and Free Ligand Concentrations Equal?

7. Deviations from Simple Binding

Macromolecular Competition Titration Method

1. Introduction

2. A Single Titration Curve: Some Simple Considerations of Possible Pitfalls

3. Quantitative Equilibrium Spectroscopic Titrations: Thermodynamic Bases

4. Nucleotide Binding to the RepA Protein of Plasmid RSF1010

5. Applying the Statistical Thermodynamic Model for the Nucleotide Binding to the RSF1010 RepA Protein Hexamer

6. Empirical Function Approach

7. MCT Method: General Considerations

8. Application of the MCT Method to the Base Specificity Problem in ASFV Pol X–ssDNA System

9. Application of MCT Method to Protein–ssDNA Lattice Binding Systems

10. Quantitative Analysis of the Binding of the E. coli DnaB Helicase to Unmodified Nucleic Acids Using the MCT Method

11. Direct Analysis of the Experimental Isotherm of Protein Ligand Binding to Two Competing Nucleic Acid Lattices

12. Using a Single Concentration of a Nonfluorescent Unmodified Nucleic Acid

13. Using Short Fluorescent Oligonucleotides in Competition with the Polymer Nucleic Acid

14. Conclusions


Analysis of PKR–RNA Interactions by Sedimentation Velocity

1. Introduction

2. Reagents and Cells

3. Experimental Design

4. Examples

5. Conclusions


Structural and Thermodynamic Analysis of PDZ–Ligand


No. of pages:
© 2011
Academic Press
eBook ISBN:
Print ISBN:

About the serial-volume-editor

Melvin Simon

Affiliations and Expertise

The Salk Institute, La Jolla, CA, USA