Preface ......................................................... v
Section I STRUCTURE PREDICTION AND ASSESSMENT METHODS .......... 1
Chapter 1 Protein Structure Modeling ........................... 3
T. Schwede, A. Sali, N. Eswar and M.C. Peitsch
Chapter 2 Protein Fold Recognition and Threading .............. 37
L. J. McGuffin
Chapter 3 Scoring Functions for Protein Structure
Prediction .......................................... 61
Francisco Melo and Ernest Feytmans
Chapter 4 Assessment of Protein Structure Predictions ......... 89
E. Capriotti and M.A. Marti-Renom
Chapter 5 The Biological Applications of Protein Models ...... 111
A. Tramontano
Section II FROM STRUCTURE TO FUNCTION TO DESIGN ............... 129
Chapter 6 Evolution of Protein Folds ......................... 131
A.N. Lupas and К.К. Koretke
Chapter 7 Classification of Protein Structures ............... 153
A. Cuff, O. Redfern and C. Orengo
Chapter 8 Methods to Characterize the Structure of Enzyme
Binding Sites ...................................... 189
A. Kahraman and J.M. Thornton
Chapter 9 Atomistic Simulations of Reactions and Transition
States ............................................. 223
M. Meuwly
Chapter 10 Functional Motions in Biomolecules: Insights from
Computational Studies at Multiple Scales ........... 253
A.W. van Wynsberghe, L. Ma, X. Chen and Q. Cui
Chapter 11 Protein-Protein Interactions and Aggregation
Processes .......................................... 299
R.I. Dima
Chapter 12 Modeling and Simulation of Ion Channels ............ 325
S. Bernèche and B. Roux
Chapter 13 Milestones in Molecular Dynamics Simulations
of RNA Systems ..................................... 363
Y. Hashem, E. Westhof and R. Auffinger
Chapter 14 Computational Protein Design ....................... 401
J.G. Saven
Chapter 15 Prediction and Identification of В Cell
Epitopes Using Protein Sequence and Structure
Information ....................................... 425
P. Andersen, D. Mkhailov and O. Lund
Chapter 16 Computational Antibody Engineering ................. 445
Т.К. Nevanen, N. Munck and U. Lamminmäki
Section III DRUG DISCOVERY AND PHARMACOLOGY ................... 467
Chapter 17 Small Molecule Docking ............................. 469
R.A. Friesner, M. Repasky and R. Farid
Chapter 18 Structure-based Pharmacophores and Screening ....... 501
R. Lewis and R.G. Karki
Chapter 19 Molecular Dynamics-based Free Energy
Simulations ........................................ 513
M.A. Cuendet, V. Zoete and O. Michielin
Chapter 20 Structure-based Computational Pharmacology and
Toxicology ......................................... 549
Angelo Vedani and Martin Smiesko
Chapter 21 Structure-based Computational Approaches
to Drug Metabolism ................................. 573
M.A. Lill
Section IV NEW FRONTIERS IN EXPERIMENTAL METHODS .............. 599
Chapter 22 New Frontiers in X-ray Crystallography ............. 601
C.U. Stirnimann and M.G. Grütter
Chapter 23 New Frontiers in High-Resolution Electron
Microscopy ......................................... 623
А. Еgel
Chapter 24 New Frontiers in Characterizing Structure and
Dynamics by NMR .................................... 655
M. Nilges, P. Markwick, T. Malliavin,
W. Rieping and M. Habeck
Section V SELECTED TOPICS ..................................... 681
Chapter 25 Docking for Neglected Diseases as Community
Efforts ............................................ 683
M. Podvinec, T. Schwede and M.C. Peitsch
Chapter 26 Protein Structure Databases ........................ 705
D. Dimitropoulos, M. John, E. Krissinel,
R. Newman and G.J. Swaminathan
Chapter 27 Molecular Graphics in Structural Biology ........... 729
A.M. Lesk, H.J. Bernstein and F.C. Bernstein
Index ......................................................... 771
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