Protein Modelling

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. In this volume, a detailed description of cutting-edge computational methods applied to protein modelling as well as specific applications are presented. Chapters include: quantum mechanical calculations on small protein models, the application of Car-Parrinello simulations to enzyme mechanisms, recent development of QM/MM methods, polarizable force fields, protein electrostatics, coarse-grained models, structure prediction of transmembrane proteins, molecular dynamics related to NMR spectroscopy, ligand docking, finite element methods for proteins as well as absorption-distribution-metabolism-excretion-toxicity prediction based on protein structures. An emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph. D. students, who need an insight into up-to-date protein modelling. A large number of descriptive, colour figures will allow the reader to get a pictorial representation of complicated structural issues.--Back cover Front Matter....Pages i-viii Introduction....Pages 1-4 Quantum Chemical Calculations on Small Protein Models....Pages 5-50 Car-Parrinello Simulations of Chemical Reactions in Proteins....Pages 51-70 Strictly Localised Molecular Orbitals in QM/MM Methods....Pages 71-89 Polarizable Force Fields for Proteins....Pages 91-134 Continuum Electrostatic Analysis of Proteins....Pages 135-163 Molecular Mechanics/Coarse-Grained Models....Pages 165-174 Modelling the Dynamic Architecture of Biomaterials Using Continuum Mechanics....Pages 175-197 Structure Prediction of Transmembrane Proteins....Pages 199-221 Dynamics of Small, Folded Proteins....Pages 223-248 Protein Ligand DockingDocking in Drug DiscoveryDrug Discovery ....Pages 249-286 ADMET Prediction Based on Protein Structures....Pages 287-322 Back Matter....Pages 323-329