Methods for SAXS-Based Structure Determination of Biomolecular Complexes

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

(2013) Ezgi Karaca et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology

(2013) Robert P. Rambo et al.   Annual Review of Biophysics

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

(2013) Dina Schneidman-Duhovny et al.   BIOPHYSICAL JOURNAL

An Unusual Topological Structure of the HIV-1 Rev Response Element

(2013) Xianyang Fang et al.   CELL

Coarse-grain modelling of protein–protein interactions

(2013) Marc Baaden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS)

(2013) Melissa A Graewert et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rapid and accurate calculation of small-angle scattering profiles using the golden ratio

(2013) Max C. Watson et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

(2013) Janosch Hennig et al.   JOURNAL OF BIOMOLECULAR NMR

Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes

(2013) Krishnakumar M. Ravikumar et al.   JOURNAL OF CHEMICAL PHYSICS

Characterization of a large glycoprotein proteoglycan by size-exclusion chromatography combined with light and X-ray scattering methods

(2013) Yasushi Watanabe et al.   JOURNAL OF CHROMATOGRAPHY A

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

(2013) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Discrete Three-Layer Stack Aggregate of a Linear Porphyrin Tetramer: Solution-Phase Structure Elucidation by NMR and X-ray Scattering

(2013) Marie Hutin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multidomain integration in the structure of the HNF-4α nuclear receptor complex

(2013) Vikas Chandra et al.   NATURE

Accurate assessment of mass, models and resolution by small-angle scattering

(2013) Robert P. Rambo et al.   NATURE

Atomic-resolution structural information from scattering experiments on macromolecules in solution

(2013) Jürgen Köfinger et al.   PHYSICAL REVIEW E

Protein recognition and selection through conformational and mutually induced fit

(2013) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cross-talk between the ligand- and DNA-binding domains of estrogen receptor

(2013) Wei Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB

(2013) Jill Trewhella et al.   STRUCTURE

Eppur Si Muove! The 2013 Nobel Prize in Chemistry

(2013) Jeremy C. Smith et al.   STRUCTURE

Discovering RNA-Protein Interactome by Using Chemical Context Profiling of the RNA-Protein Interface

(2013) Marc Parisien et al.   Cell Reports

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials

(2012) Haiguang Liu et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution

(2012) Clement E. Blanchet et al.   Annual Review of Physical Chemistry

Conformational Analysis of a Genetically Encoded FRET Biosensor by SAXS

(2012) Haydyn D.T. Mertens et al.   BIOPHYSICAL JOURNAL

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

(2012) Krishnakumar M. Ravikumar et al.   BIOPHYSICAL JOURNAL

MD–SAXS method with nonspherical boundaries

(2012) Tomotaka Oroguchi et al.   CHEMICAL PHYSICS LETTERS

Advances in X-ray scattering: from solution SAXS to achievements with coherent beams

(2012) Javier Pérez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Determining RNA three-dimensional structures using low-resolution data

(2012) Marc Parisien et al.   JOURNAL OF STRUCTURAL BIOLOGY

Modeling Detergent Organization around Aquaporin-0 Using Small-Angle X-ray Scattering

(2012) Alice Berthaud et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Predictive energy landscapes for protein-protein association

(2012) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X-ray lasers for structural and dynamic biology

(2012) J C H Spence et al.   REPORTS ON PROGRESS IN PHYSICS

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function

(2012) Michael A. Jamros et al.   PLoS Computational Biology

The structural plasticity of the human copper chaperone for SOD1: insights from combined size-exclusion chromatographic and solution X-ray scattering studies

(2011) Gareth S. A. Wright et al.   BIOCHEMICAL JOURNAL

Improving Protein Template Recognition by Using Small-Angle X-Ray Scattering Profiles

(2011) Marcelo Augusto dos Reis et al.   BIOPHYSICAL JOURNAL

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell

(2011) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering

(2011) Michael D. Daily et al.   CHEMICAL PHYSICS

Structural basis of p38α regulation by hematopoietic tyrosine phosphatase

(2011) Dana M Francis et al.   Nature Chemical Biology

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

(2011) Frédéric Poitevin et al.   NUCLEIC ACIDS RESEARCH

Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy

(2011) E. Boura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

EROS: Better than SAXS!

(2011) Sichun Yang et al.   STRUCTURE

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

Modeling the Hydration Layer around Proteins: HyPred

(2010) Jouko J. Virtanen et al.   BIOPHYSICAL JOURNAL

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

(2010) Kasper Stovgaard et al.   BMC BIOINFORMATICS

Proteins at Work

(2010) Michael A. Jamros et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Structure Determination Using SAXS Data

(2010) Sichun Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Macromolecular docking restrained by a small angle X-ray scattering profile

(2010) Dina Schneidman-Duhovny et al.   JOURNAL OF STRUCTURAL BIOLOGY

Multistage Collapse of a Bacterial Ribozyme Observed by Time-Resolved Small-Angle X-ray Scattering

(2010) Joon Ho Roh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improved Fitting of Solution X-ray Scattering Data to Macromolecular Structures and Structural Ensembles by Explicit Water Modeling

(2010) Alexander Grishaev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering

(2010) Yun-Xing Wang et al.   METHODS

Proteins in dynamic equilibrium

(2010) Pau Bernadó et al.   NATURE

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Multidomain assembled states of Hck tyrosine kinase in solution

(2010) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Coarse Residue-Based Computational Method for X-Ray Solution Scattering Characterization of Protein Folds and Multiple Conformational States of Large Protein Complexes

(2009) Sichun Yang et al.   BIOPHYSICAL JOURNAL

Structure and flexibility within proteins as identified through small angle X-ray scattering

(2009) M. Pelikan et al.   GENERAL PHYSIOLOGY AND BIOPHYSICS

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

(2009) Jaydeep Bardhan et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline

(2009) G. David et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Simulated x-ray scattering of protein solutions using explicit-solvent models

(2009) Sanghyun Park et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of Multicomponent Protein Structures in Solution Using Global Orientation and Shape Restraints

(2009) Jinbu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

(2009) Greg L Hura et al.   NATURE METHODS

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Experimental approaches for solution X-ray scattering and fiber diffraction

(2008) H Tsuruta et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Reconstructing three-dimensional shape envelopes from time-resolved small-angle X-ray scattering data

(2008) Jessica Lamb et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies

(2008) Friedrich Förster et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Structures of Full-Length p97, an AAA ATPase: Implications for Mechanisms of Nucleotide-Dependent Conformational Change

(2008) Jason M. Davies et al.   STRUCTURE

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY