Description 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.
Contents
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.
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