Algorithms in Structural Molecular Biology
Published on 15. August 2023
Book
Paperback/Softback
464 pages
978-0-262-54879-3 (ISBN)
Description
An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules.
Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility.
The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility.
The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
More details
Series
Language
English
Place of publication
Cambridge (Massachusetts)
United States
Publishing group
MIT Press Ltd
Target group
College/higher education
Interest Age: From 18 years
Product notice
Paperback (trade)
Illustrations
163 B&W ILLUS., 11 TABLES, 52
Dimensions
Height: 229 mm
Width: 203 mm
Thickness: 27 mm
Weight
953 gr
ISBN-13
978-0-262-54879-3 (9780262548793)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Person
Content
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
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