Computational Structural Biology: Methods and Applications Book

Sect. I Structure Prediction and Assessment Methods 1

Ch. 1 Protein Structure Modeling T. Schwede Schwede, T. A. Sali Sali, A. N. Eswar Eswar, N. M. C. Peitsch Peitsch, M. C. 3

Ch. 2 Protein Fold Recognition and Threading L. J. McGuffin McGuffin, L. J. 37

Ch. 3 Scoring Functions for Protein Structure Prediction Francisco Melo Melo, Francisco Ernest Feytmans Feytmans, Ernest 61

Ch. 4 Assessment of Protein Structure Predictions E. Capriotti Capriotti, E. M. A. Marti-Renom Marti-Renom, M. A. 89

Ch. 5 The Biological Applications of Protein Models A. Tramontano Tramontano, A. 111

Sect. II From Structure to Function to Design 129

Ch. 6 Evolution of Protein Folds A. N. Lupas Lupas, A. N. K. K. Koretke Koretke, K. K. 131

Ch. 7 Classification of Protein Structures A. Cuff Cuff, A. O. Redfern Redfern, O. C. Orengo Orengo, C. 153

Ch. 8 Methods to Characterize the Structure of Enzyme Binding Sites A. Kahraman Kahraman, A. J. M. Thornton Thornton, J. M. 189

Ch. 9 Atomistic Simulations of Reactions and Transition States M. Meuwly Meuwly, M. 223

Ch. 10 Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales A. W. van Wynsberghe van Wynsberghe, A. W. L. Ma Ma, L. X. Chen Chen, X. Q. Cui Cui, Q. 253

Ch. 11 Protein-Protein Interactions and Aggregation Processes R. I. Dima Dima, R. I. 299

Ch. 12 Modeling and Simulation of Ion Channels S. Berneche Berneche, S. B. Roux Roux, B. 325

Ch. 13 Milestones in Molecular Dynamics Simulations of RNA Systems Y. Hashem Hashem, Y. E. Westhof Westhof, E. P. Auffinger Auffinger, P. 363

Ch. 14 Computational Protein Design J. G. Saven Saven, J. G. 401

Ch. 15 Prediction and Identification of B Cell EpitopesUsing Protein Sequence and Structure Information P. Andersen Andersen, P. D. Mkhailov Mkhailov, D. O. Lund Lund, O. 425

Ch. 16 Computational Antibody Engineering T. K. Nevanen Nevanen, T. K. N. Munck Munck, N. U. Lamminmaki Lamminmaki, U. 445

Sect. III Drug Discovery and Pharmacology 467

Ch. 17 Small Molecule Docking R. A. Friesner Friesner, R. A. M. Repasky Repasky, M. R. Farid Farid, R. 469

Ch. 18 Structure-based Pharmacophores and Screening R. Lewis Lewis, R. R. G. Karki Karki, R. G. 501

Ch. 19 Molecular Dynamics-based Free Energy Simulations M. A. Cuendet Cuendet, M. A. V. Zoete Zoete, V. O. Michielin Michielin, O. 513

Ch. 20 Structure-based Computational Pharmacology and Toxicology Angelo Vedani Vedani, Angelo Martin Smiesko Smiesko, Martin 549

Ch. 21 Structure-based Computational Approaches to Drug Metabolism M. A. Lill Lill, M. A. 573

Sect. IV New Frontiers in Experimental Methods 599

Ch. 22 New Frontiers in X-ray Crystallography C. U. Stirnimann Stirnimann, C. U. M. G. Grutter Grutter, M. G. 601

Ch. 23 New Frontiers in High-Resolution Electron Microscopy A. Engel Engel, A. 623

Ch. 24 New Frontiers in Characterizing Structure and Dynamics by NMR M. Nilges Nilges, M. P. Markwick Markwick, P. T. Malliavin Malliavin, T. W. Rieping Rieping, W. M. Habeck Habeck, M. 655

Sect. V Selected Topics 681

Ch. 25 Docking for Neglected Diseases as Community Efforts M. Podvinec Podvinec, M. T. Schwede Schwede, T. M. C. Peitsch Peitsch, M. C. 683

Ch. 26 Protein Structure Databases D. Dimitropoulos Dimitropoulos, D. M. John John, M. E. Krissinel Krissinel, E. R. Newman Newman, R. G. J. Swaminathan Swaminathan, G. J. 705

Ch. 27 Molecular Graphics in Structural Biology A. M. Lesk Lesk, A. M. H. J. Bernstein Bernstein, H. J. F. C. Bernstein Bernstein, F. C. 729

Index 771