Chapter 1. Hybrid potentials for large molecular systems (P. Amara, M.J. Field).Introduction.Hybrid potentials.Challenges.Applications.Conclusions.2. Proton transfer in models biomolecules (S. Scheiner).Introduction.Intrinsic proton transfer properties.Hydrogen bond length.Hydrogen bond angles.Reversals in relative pKa.Environmental effects.Very strong hydrogen bonds.3. Computational approaches to the studies of the interactions of nucleic acid bases (J Spōner, P. Hobza, J. Leszczynski).Introduction.Historical overview of ab initio studies on nucleic acid base pairs.Methods.Results.Concluding remarks.4. Nucleic acid bases in solution (M. Orozco, E. Cubero, X. Barril, C. Colominas, F.J. Luque).The solvent.Computational approaches to solvation.The effect of solvent on nucleic acid bases.Conclusion.5. Current trends in modeling interactions of DNA fragments with polar solvents (L. Gorb, J. Leszczynski).Introduction.Continuum models of solvation.Supermolecular approximation.The hydration of the prototypic molecules.The hydration of heterocycles - parent compounds of DNA bases.Hydration of the DNA bases.Hydration of DNA base pairs.Conclusion.6. Radiation-induced DNA damage and repair: An approach from ab initio MO method (M. Aida, M. Kaneko, M. Dupuis).Introduction.Structures of pyrimidine dimers.Characteristics of thymine dimer.Fragmentation mechanism of T 〈〉 T(˙ +).Other pyrimidine dimers.Conclusion.7. Application of molecular orbital theory to elucidation of radical processes induced by radiation damage to DNA (A.-O. Colson, M.D. Sevilla).Background.Individual DNA bases.Base pairs.Base pair stacking.Effect of waters of hydration.Sugar-phosphate backbone.DNA base H ˙ and ˙ OH adduct radicals.Radioprotection.8. Exploring the structural repertoire of Guanine-rich DNA sequences: Computer modeling studies (M. Bansal, M. Ravikiran, S. Chowdhury).Introduction.Guanine rich triple helical structures.Parallel and folded back quadruplex structures.Conclusions.9. The calculation of relative binding thermodynamics of molecular associations in aqueous environments (G.J. Tawa, I.A. Topol, S.K. Burt).Introduction.Theory.Computational protocol.The relative binding free energies of peptidic inhibitors to HIV-1 protease and its I84V mutant.Concluding remarks.10. Theoretical tools for analysis and modeling electrostatic effects in biomolecules (W.A. Sokalski, P. Kędierski, J. Grembecka, P. Dziedoński, K. Strasburger).Introduction.Methods.Applications.Conclusions.11. Application of reduced models to protein structure prediction (J. Skolnick, A. Kolinski, A.R. Ortiz).Introduction.Exact restraint models.Tertiary structure predictions by ab initio model building.What is the requisite resolution of predicted structures?.Techniques for low to high resolution modeling.Role of structure prediction in the genomics revolution.Outlook.12. Modeling DNA-protein interactions (K. Zakrzewska, R. Lavery).The first steps.Analysing protein-DNA recognition.Molecular mechanics and dynamics simulations.Protein-DNA docking.The next steps.13. Interactions of small molecules and peptides with membranes (A. Pohorille, M.A. Wilson, C. Chipot, M.H. New, K. Schwieghofer).Introduction.Approach.Transport of small solutes and ions across membrane interfaces.Interactions of peptides and membranes.Hydration forces.Conclusions and future directions.14. Modeling of antifreeze proteins (J.D. Madura, A. Wierzbicki).Introduction.Modeling AFPS on ice.Simulations of AFPS with explicit water.Simulations of AFPS in a continuum.Simulations of the Winter Flounder in the ice/water interface.Summary.15. The role of computational techniques in retrometabolic drug design strategies (N. Bodor, P. Buchwald, M.-J. Huang).Introduction.Principles of retrometabolic drug design.Predicting properties.Soft drugs.Computer-aided design.Chemical delivery systems.Conclusions.16. Computational aspects of neural membrane biophysics (R. Wallace).Introduction.Algorithmic complexity and the principles of molecular computing.Membrane studies in cell biology.Hydrophobic mismatch: a candidate mechanism for neuromolecular computing.Hydrophobic mismatch and molecular computation.Genetic regulation of neuromolecular computing.Potential experiments in neuromolecular computation.Conclusion.Index.