Algorithms in Structural Molecular Biology (Paperback)

Preface xxiii
Acknowledgments xxxi
1 Introduction to Protein Structure and NMR 1
2 Basic Principles of NMR 7
3 Proteins and NMR Structural Biology 15
4 MBM, SVD, PCA, and RDCs 23
5 Principal Components Analysis, Residual Dipolar Couplings, and Their Relationship in NMR Structural Biology 27
6 Orientational Structures of Native and Denatured Proteins Using RDCs 53
7 Solution Structures of Native and Denatured Proteins Using RDCs 53
8 JIGSAW and NMR 59
9 Peptide Design 67
10 Protein Interface and Active Site Redesign 77
11 Computational Protein Design 87
12 Nonribosomal Code and K* Algorithms for Ensemble-Based Protein Design 97
13 RDCs in NMR Structural Biology 115
14 Nuclear Vector Replacement 119
15-18 Short Course: Automated NMR Assignment and Protein Structure Determination Using Sparse Residual Dipolar Couplings 127
19 Proteomic Disease Classification Algorithm 187
20 Protein Flexibility: Introduction to Inverse Kinematics and the Loop Closure Problem 191
21 Normal Mode Analysis (NMA) and Rigidity Theory 197
22 ROCK and FRODA for Protein Flexibility 205
23 Applications of NMA to Protein-Protein and Ligand-Protein Binding 213
24 Modeling Equilibrium Fluctuations in Proteins 219
25 Generalized Belief Propagation, Free Energy Approximations, and Protein Design 227
26 Ligand Configurational Entropy 245
27 Carrier Protein Structure and Recognition in Peptide Biosynthesis 249
28 Kinetic Studies of the Initial Module PheATE of Gramicidin S Synthetase 253
29 Protein-Ligand NOE Matching 259
30 Side-Chain and Backbone Flexibility in Protein Core Design 265
31 Distance Geometry 273
32 Distance Geometry: NP-Hard, NP-Hard to Approximate 279
33 A Topology-Constrained Network Algorithm for NOESY Data Interpretation 285
34 MARS: An Algorithm for Backbone Resonance Assignment 293
35 Errors in Structure Determination by NMR Spectroscopy 301
36 SemiDefinite Programming and Distance Geometry with Orientation Constraints 307
37 Graph Cuts for Energy Minimization and Assignment Problems 315
38 Classifying the Power of Graph Cuts for Energy Minimization 323
39 Protein Unfolding by Using Residual Dipolar Couplings 333
40 Structure-Based Protein-Ligand Binding 341
41 Flexible Ligand-Protein Docking 345
42 Analyzing Protein Structures Using and Ensemble Representation 351
43 NMR Resonance Assignment Assisted by Mass Spectrometry 355
44 Autolink: An Algorithm for Automated NMR Resonance Assignment 363
45 CS-Rosetta: Protein Structure Generalization from NMR Chemical Shift Data 371
46 Enzyme Redesign by SVM 377
47 Cross-Rotation Analysis Algorithm 383
48 Molecular Replacement and NCS in X-ray Crystallography 387
49 Optimization of Surface Charge-Charge Interactions 393
50 Computational Topology and Protein Structure 399
Index 415