Molecular Modeling of Proteins Book

Preface     v
Contributors     ix
Methodology
Molecular Dynamics Simulations   Erik R. Lindahl     3
Monte Carlo Simulations   David J. Earl   Michael W. Deem     25
Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes   Jiali Gao   Dan T. Major   Yao Fan   Yen-lin Lin   Shuhua Ma   Kin-Yiu Wong     37
Comparison of Protein Force Fields for Molecular Dynamics Simulations   Olgun Guvench   Alexander D. MacKerell, Jr.     63
Normal Modes and Essential Dynamics   Steven Hayward   Bert L. de Groot     89
Free Energy Calculations
Calculation of Absolute Protein-Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method   Hyung-June Woo     109
Free Energy Calculations Applied to Membrane Proteins   Christophe Chipot     121
Molecular Modeling of Membrane Proteins
Molecular Dynamics Simulations of Membrane Proteins   Philip C. Biggin   Peter J. Bond     147
Membrane-Associated Proteins and Peptides   Marc F. Lensink     161
Implicit Membrane Models for Membrane Protein Simulation   Michael Feig     181
Protein Structure Determination
Comparative Modeling of Proteins   Gerald H. Lushington     199
Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints   Andrew J. Beevers   Andreas Kukol     213
Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes   Gloria Fuentes   Aalt D.J. van Dijk   Alexandre M.J.J. Bonvin     229
Conformational Change
Conformational Changes in Protein Function   Haiguang Liu   Shubhra Ghosh Dastidar   Hongxing Lei   Wei Zhang   Matthew C. Lee   Yong Duan     259
Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations   Hongxing Lei   Yong Duan     277
Modeling of Protein Misfolding in Disease   Edyta B. Malolepsza     297
Applications to Drug Design
Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking   David S. Wishart     333
Receptor Flexibility for Large-Scale In Silico Ligand Screens: Chances and Challenges   B. Fischer   H. Merlitz   W. Wenzel     353
Molecular Docking   Garrett M. Morris   Marguerita Lim-Wilby     365
Index     383