Algorithms in structural molecular biology / Bruce R. Donald.

Format:

Book

Author/Creator:

Donald, Bruce R.

Series:

Computational molecular biology.

Computational molecular biology

Language:

English

Subjects (All):

Biophysics--Mathematical models.

Biophysics.

Physical Description:

xxx, 429 p., [32] p. of plates : ill. (some col.).

Edition:

1st ed.

Place of Publication:

Cambridge, Mass. : MIT Press, c2011.

Language Note:

English

Summary:

An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.

Contents:

Cover

Brief Contents

Contents

Preface

Acknowledgments

1 Introduction to Protein Structure and NMR

2 Basic Principles of NMR

3 Proteins and NMR Structural Biology

4 MBM, SVD, PCA, and RDCs

5 Principal Components Analysis, Residual Dipolar Couplings, and Their Relationship in NMR Structural Biology

6 Orientational Sampling of Interatomic Vectors

7 Solution Structures of Native and Denatured Proteins Using RDCs

8 JIGSAW and NMR

9 Peptide Design

10 Protein Interface and Active Site Redesign

11 Computational Protein Design

12 Nonribosomal Code and K* Algorithms for Ensemble-Based Protein Design

13 RDCs in NMR Structural Biology

14 Nuclear Vector Replacement

15-18 Short Course: Automated NMR Assignment and Protein Structure Determination Using Sparse Residual Dipolar Couplings

19 Proteomic Disease Classification Algorithm

20 Protein Flexibility: Introduction to Inverse Kinematics and Loop Closure Problem

21 Normal Mode Analysis (NMA) and Rigidity Theory

22 ROCK and FRODA for Protein Flexibility

23 Applications of NMA to Protein-Protein and Ligand-Protein Binding

24 Modeling Equilibrium Fluctuations in Proteins

25 Generalized Belief Propagation, Free Energy Approximations, and Protein Design

26 Ligand Configurational Entropy

27 Carrier Protein Structure and Recognition in Peptide Biosynthesis

28 Kinetic Studies of the Initial Module PheATE of Gramicidin S Synthetase

29 Protein-Ligand NOE Matching

30 Side-Chain and Backbone Flexibility in Protein Core Design

31 Distance Geometry

32 Distance Geometry: NP-Hard, NP-Hard to Approximate

33 A Topology-Constrained Network Algorithm for NOESY Data Interpretation

34 MARS: An Algorithm for Backbone Resonance Assignment

35 Errors in Structure Determination by NMR Spectroscopy.

36 SemiDefinite Programming and Distance Geometry with Orientation Constraints

37 Graph Cuts for Energy Minimization and Assignment Problems

38 Classifying the Power of Graph Cuts for Energy Minimization

39 Protein Unfolding by Using Residual Dipolar Couplings

40 Structure-Based Protein-Ligand Binding

41 Flexible Ligand-Protein Docking

42 Analyzing Protein Structures Using an Ensemble Representation

43 NMR Resonance Assignment Assisted by Mass Spectrometry

44 Autolink: An Algorithm for Automated NMR Resonance Assignment

45 CS-Rosetta: Protein Structure Generation from NMR Chemical Shift Data

46 Enzyme Redesign by SVM

47 Cross-Rotation Analysis Algorithm

48 Molecular Replacement and NCS in X-ray Crystallography

49 Optimization of Surface Charge-Charge Interactions

50 Computational Topology and Protein Structure

Index

Insert.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Includes bibliographical references and index.

ISBN:

0-262-29872-4

OCLC:

759040881