T. Schwede and A. Sali and N. Eswar and M. C. PeitschL. J. McGuffinFrancisco Melo and Ernest FeytmansE. Capriotti and M. A. Marti-RenomA. TramontanoA. N. Lupas and K. K. KoretkeA. Cuff and O. Redfern and C. OrengoA. Kahraman and J. M. ThorntonM. MeuwlyA. W. van Wynsberghe and L. Ma and X. Chen and Q. CuiR. I. DimaS. Berneche and B. RouxY. Hashem and E. Westhof and P. AuffingerJ. G. SavenP. Andersen and D. Mkhailov and O. LundT. K. Nevanen and N. Munck and U. LamminmakiR. A. Friesner and M. Repasky and R. FaridR. Lewis and R. G. KarkiM. A. Cuendet and V. Zoete and O. MichielinAngelo Vedani and Martin SmieskoM. A. LillC. U. Stirnimann and M. G. GrutterA. EngelM. Nilges and P. Markwick and T. Malliavin and W. Rieping and M. HabeckM. Podvinec and T. Schwede and M. C. PeitschD. Dimitropoulos and M. John and E. Krissinel and R. Newman and G. J. SwaminathanA. M. Lesk and H. J. Bernstein and F. C. Bernstein

Preface	p. v
Section I Structure Prediction and Assessment Methods	p. 1
Chapter 1 Protein Structure Modeling	p. 3
Chapter 2 Protein Fold Recognition and Threading	p. 37
Chapter 3 Scoring Functions for Protein Structure Prediction	p. 61
Chapter 4 Assessment of Protein Structure Predictions	p. 89
Chapter 5 The Biological Applications of Protein Models	p. 111
Section II From Structure to Function to Design	p. 129
Chapter 6 Evolution of Protein Folds	p. 131
Chapter 7 Classification of Protein Structures	p. 153
Chapter 8 Methods to Characterize the Structure of Enzyme Binding Sites	p. 189
Chapter 9 Atomistic Simulations of Reactions and Transition States	p. 223
Chapter 10 Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales	p. 253
Chapter 11 Protein-Protein Interactions and Aggregation Processes	p. 299
Chapter 12 Modeling and Simulation of Ion Channels	p. 325
Chapter 13 Milestones in Molecular Dynamics Simulations of RNA Systems	p. 363
Chapter 14 Computational Protein Design	p. 401
Chapter 15 Prediction and Identification of B Cell Epitopes Using Protein Sequence and Structure Information	p. 425
Chapter 16 Computational Antibody Engineering	p. 445
Section III Drug Discovery and Pharmacology	p. 467
Chapter 17 Small Molecule Docking	p. 469
Chapter 18 Structure-based Pharmacophores and Screening	p. 501
Chapter 19 Molecular Dynamics-based Free Energy Simulations	p. 513
Chapter 20 Structure-based Computational Pharmacology and Toxicology	p. 549
Chapter 21 Structure-based Computational Approaches to Drug Metabolism	p. 573
Section IV New Frontiers in Experimental Methods	p. 599
Chapter 22 New Frontiers in X-ray Crystallography	p. 601
Chapter 23 New Frontiers in High-Resolution Electron Microscopy	p. 623
Chapter 24 New Frontiers in Characterizing Structure and Dynamics by NMR	p. 655
Section V Selected Topics	p. 681
Chapter 25 Docking for Neglected Diseases as Community Efforts	p. 683
Chapter 26 Protein Structure Databases	p. 705
Chapter 27 Molecular Graphics in Structural Biology	p. 729
Index	p. 771