Protein Modelling

1. Front Matter

   Pages i-viii

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2. Introduction

   • Gábor Náray-Szabó

   Pages 1-4

3. Quantum Chemical Calculations on Small Protein Models

   • Imre Jákli, András Perczel, Béla Viskolcz, Imre G. Csizmadia

   Pages 5-50

4. Car-Parrinello Simulations of Chemical Reactions in Proteins

   • Carme Rovira

   Pages 51-70

5. Strictly Localised Molecular Orbitals in QM/MM Methods

   • György G. Ferenczy, Gábor Náray-Szabó

   Pages 71-89

6. Polarizable Force Fields for Proteins

   • Oleg Khoruzhii, Oleg Butin, Alexey Illarionov, Igor Leontyev, Mikhail Olevanov, Vladimir Ozrin et al.

   Pages 91-134

7. Continuum Electrostatic Analysis of Proteins

   • G. Matthias Ullmann, Elisa Bombarda

   Pages 135-163

8. Molecular Mechanics/Coarse-Grained Models

   • Alejandro Giorgetti, Paolo Carloni

   Pages 165-174

9. Modelling the Dynamic Architecture of Biomaterials Using Continuum Mechanics

   • Robin Oliver, Robin A. Richardson, Ben Hanson, Katherine Kendrick, Daniel J. Read, Oliver G. Harlen et al.

   Pages 175-197

10. Structure Prediction of Transmembrane Proteins

    • Gábor E. Tusnády, Dániel Kozma

    Pages 199-221

11. Dynamics of Small, Folded Proteins

    • Petra Rovó, Dóra K. Menyhárd, Gábor Náray-Szabó, András Perczel

    Pages 223-248

12. Protein Ligand Docking in Drug Discovery

    • N. F. Brás, N. M. F. S. A. Cerqueira, S. F. Sousa, P. A. Fernandes, M. J. Ramos

    Pages 249-286

13. ADMET Prediction Based on Protein Structures

    • Ákos Tarcsay, György M. Keserű

    Pages 287-322

14. Back Matter

    Pages 323-329

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In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.

• Enzymes Mode of Action
• Protein Design
• Protein Dynamics and Function
• Protein Modelling Software

• Chemistry Department, Eotvos Lorand University, Budapest, Hungary

  Gábor Náray-Szabó

Hungarian chemist, professor, member of the Hungarian Academy of Sciences, from 1996 to 1999, Deputy Secretary General. The theoretical chemistry and structural biology renowned researcher. Between 2006 and 2013, was the Director General of the Academy Library.

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