Computational Molecular Biology

This book covers applications of computational techniques to biological problems. These techniques are based by an ever-growing number of researchers with different scientific backgrounds - biologists, chemists, and physicists.

The rapid development of molecular biology in recent years has been mirrored by the rapid development of computer hardware and software. This has resulted in the development of sophisticated computational techniques and a wide range of computer simulations involving such methods. Among the areas where progress has been profound is in the modeling of DNA structure and function, the understanding at a molecular level of the role of solvents in biological phenomena, the calculation of the properties of molecular associations in aqueous solutions, computationally assisted drug design, the prediction of protein structure, and protein - DNA recognition, to mention just a few examples. This volume comprises a balanced blend of contributions covering such topics. They reveal the details of computational approaches designed for biomoleucles and provide extensive illustrations of current applications of modern techniques.

A broad group of readers ranging from beginning graduate students to molecular biology professions should be able to find useful contributions in this selection of reviews.

Chapter 1. Hybrid potentials for large molecular systems.


2. Proton transfer in models biomolecules.


3. Computational approaches to the studies of the interactions of nucleic acid bases.


4. Nucleic acid bases in solution.


5. Current trends in modeling interactions of DNA fragments with polar solvents.


6. Radiation-induced DNA damage and repair: An approach from ab initio MO method.

7. Application of molecular orbital theory to elucidation of radical processes induced by radiation damage to DNA.

8. Exploring the structural repertoire of Guanine-rich DNA sequences: Computer modeling studies.

9. The calculation of relative binding thermodynamics of molecular associations in aqueous environments.

10. Theoretical tools for analysis and modeling electrostatic effects in biomolecules.


11. Application of reduced models to protein structure prediction.


12. Modeling DNA-protein interactions.


13. Interactions of small molecules and peptides with membranes.


14. Modeling of antifreeze proteins.


15. The role of computational techniques in retrometabolic drug design strategies.


16. Computational aspects of neural membrane biophysics.

Index.