
Scattering Methods in Structural Biology Part B
- 1st Edition, Volume 678 - January 11, 2023
- Imprint: Academic Press
- Editor: John Tainer
- Language: English
- Hardback ISBN:9 7 8 - 0 - 3 2 3 - 9 9 1 8 1 - 0
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 9 1 8 2 - 7
Scattering Methods in Structural Biology, Part B, Volume 676 in the Methods in Enzymology serial, highlights advances in the field, presenting chapters on Quality controls, Refin… Read more

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Request a sales quoteScattering Methods in Structural Biology, Part B, Volume 676 in the Methods in Enzymology serial, highlights advances in the field, presenting chapters on Quality controls, Refining biomolecular structures and ensembles by SAXS-driven molecular dynamics simulations, Data analysis and modelling of small-angle scattering data with contrast variation, Observing protein degradation in solution by the PAN-20S proteasome complex: state-of-the-art and future perspectives of TR-SANS as a complementary tool to NMR, crystallography and Cryo-EM, Extracting structural insights from chemically-specific soft X-ray scattering, Reconstruction of 3D density of biological macromolecules from solution scattering, ATSAS- present state and new developments in computational methods, and much more.
Additional chapters cover Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles (FoXSDock and MultiFoXS), Validation of macromolecular flexibility in solution by SAXS, Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes, Application of Molecular Simulation Methods to Analyze SAS Data, and more.
- Provides the authority and expertise of leading contributors from an international board of authors
- Presents the latest release in the Methods in Enzymology serial
- Updated release includes the latest information on Small Angle Scattering Methods for Structural Interpretation
- Cover image
- Title page
- Table of Contents
- Copyright
- Contributors
- Preface
- Chapter One: Data quality assurance, model validation, and data sharing for biomolecular structures from small-angle scattering
- Abstract
- 1: Becoming a mainstream structural biology technique
- 2: The path to standards and data sharing
- 3: Draft publication guidelines and plans for data archiving
- 4: A data archive for SAS as part of a federated system for integrative structural biology
- 5: The current publication guidelines and data archiving requirements
- 6: Quantifying data reproducibility and establishing a consensus experimental benchmark data set
- 7: Future opportunities
- 8: Conclusions
- Acknowledgments
- References
- Chapter Two: Structure and ensemble refinement against SAXS data: Combining MD simulations with Bayesian inference or with the maximum entropy principle
- Abstract
- 1: Introduction
- 2: SAXS-driven molecular dynamics simulations
- 3: SAXS-driven MD as a tool for Bayesian inference of molecular structures
- 4: Maximum-entropy ensemble refinement against SAXS data
- 5: Discussion: Conceptual considerations and recommendations
- 6: Applications
- 7: Summary
- References
- Chapter Three: Data analysis and modeling of small-angle neutron scattering data with contrast variation from bio-macromolecular complexes
- Abstract
- 1: Introduction
- 2: Analysis of the forward scattering intensity, I(0), and calculation of contrast
- 3: Analysis of the radius of gyration
- 4: Composite scattering functions
- 5: Dummy-atom (bead) modeling against contrast variation data
- 6: Rigid body modeling against contrast variation data
- 7: Summary
- Acknowledgments
- References
- Chapter Four: Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS
- Abstract
- 1: The interest of TR-SANS for dynamic bio-macromolecular systems
- 2: Specific protein degradation in biological cells
- 3: A concrete example of bio-macromolecular TR-SANS: Insight into structural dynamics of substrate processing by the archaeal PAN-proteasome system
- 4: Sample conditions, instrumental setup and data reduction
- 5: Experimental TR-SANS results and mechanistic model of protein degradation
- 6: Conclusions and outlook
- Acknowledgments
- References
- Chapter Five: Extracting structural insights from soft X-ray scattering of biological assemblies
- Abstract
- 1: Introduction
- 2: Predicting RSoXS scattering contrast from NEXAFS spectra
- 3: Reduction of RSoXS 2D data into 1D
- 4: Interpretation of scattering data
- 5: Identification of the real-space structure that leads to an observed scattering profile
- 6: Opportunities for application of new RSoXS analysis approaches to biological assemblies
- 7: Conclusion and outlook
- Acknowledgments
- References
- Chapter Six: Reconstruction of 3D density from solution scattering
- Abstract
- 1: Introduction
- 2: Theory
- 3: DENSS software
- 4: Preparing the data with denss.fit_data.py
- 5: Running a single reconstruction with denss.py
- 6: Alignment and averaging
- 7: Analysis and interpretation of results
- 8: SANS
- 9: Materials science applications
- 10: Publication guidelines and SASBDB deposition
- 11: Summary
- References
- Chapter Seven: Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS
- Abstract
- 1: Introduction
- 2: Calculation and simulation of scattering data
- 3: Primary data processing
- 4: Structural modeling from SAXS data
- 5: ATSAS summary
- References
- Chapter Eight: Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models
- Abstract
- 1: Introduction
- 2: Materials and methods
- 3: Results
- 4: Protocol
- 5: Discussion
- Acknowledgments
- References
- Chapter Nine: Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes
- Abstract
- 1: Introduction
- 2: Sample preparation
- 3: NMR spectroscopy
- 4: Small angle X-ray and neutron scattering (SAXS/SANS)
- 5: Integration of NMR and SAS
- 6: Conclusions and future perspectives
- Acknowledgments
- References
- Chapter Ten: From dilute to concentrated solutions of intrinsically disordered proteins: Interpretation and analysis of collected data
- Abstract
- 1: Introduction
- 2: How to tell if a protein is an IDP?
- 3: The conformational ensemble
- 4: Ensemble optimization methods
- 5: Special considerations for crowded IDP solutions
- 6: Beyond analytical models
- 7: General notes on the treatment of hydration layers of IDPs
- 8: Summary and conclusions
- Acknowledgments
- References
- Chapter Eleven: Applying HT-SAXS to chemical ligand screening
- Abstract
- 1: Introduction
- 2: Considerations for SAXS target and library selection
- 3: HT-SAXS sample preparation
- 4: Benchmarking a pilot HT-SAXS screen
- 5: Ligand screen design and assembly
- 6: Analysis of HT-SAXS screening datasets
- 7: Summary and future perspectives
- Simple Scattering deposition
- Acknowledgments
- References
- Chapter Twelve: Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution
- Abstract
- 1: Introduction
- 2: Obtaining a protein structure prediction
- 3: Prediction of SAXS curve from an atomic model
- 4: Comparison of experimental and predicted SAXS curves
- 5: Fitting of the protein structure prediction(s) to the experimental SAXS data
- 6: Example: XRCC1 solution state
- 7: Notes
- 8: Summary and conclusions
- Acknowledgments
- References
- Chapter Thirteen: Protein fibrillation from another small angle—SAXS data analysis of developing systems
- Abstract
- 1: Introduction
- 2: General method notes
- 3: Essential check of SAXS data from fibrillating systems
- 4: Initial analysis of the background subtracted data
- 5: Decomposition of data—Manual approach
- 6: Decomposition of developing data using COSMiCS
- 7: Further interpretation
- 8: Alternative approaches
- 9: Summary and conclusions
- Acknowledgments
- References
- Chapter Fourteen: Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources
- Abstract
- 1: Introduction
- 2: Visualization of correlated SAXS data
- 3: Simple Scattering data set repository
- 4: Summary and outlook
- Acknowledgments
- References
- Edition: 1
- Volume: 678
- Published: January 11, 2023
- Imprint: Academic Press
- No. of pages: 460
- Language: English
- Hardback ISBN: 9780323991810
- eBook ISBN: 9780323991827
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