Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods

(2021) Mustapha Carab Ahmed et al.   Frontiers in Molecular Biosciences

Correlated Motions in Structural Biology

(2021) Da Xu et al.   BIOCHEMISTRY

Experimental noise in small-angle scattering can be assessed using the Bayesian indirect Fourier transformation

(2021) Andreas Haahr Larsen et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Automatic Bayesian Weighting for SAXS Data

(2021) Yannick G. Spill et al.   Frontiers in Molecular Biosciences

Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data

(2020) Christopher Prior et al.   Journal of Chemical Theory and Computation

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

(2020) Andreas Haahr Larsen et al.   PLoS Computational Biology

Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

(2020) James Lincoff et al.   Communications Chemistry

Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?

(2019) S. Jephthah et al.   Journal of Chemical Theory and Computation

SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy

(2019) Markus R. Hermann et al.   Journal of Chemical Theory and Computation

Interpreting solution X-ray scattering data using molecular simulations

(2018) Jochen S Hub   CURRENT OPINION IN STRUCTURAL BIOLOGY

The geometry of protein hydration

(2018) Filip Persson et al.   JOURNAL OF CHEMICAL PHYSICS

An Extended Guinier Analysis for Intrinsically Disordered Proteins

(2018) Wenwei Zheng et al.   JOURNAL OF MOLECULAR BIOLOGY

On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations

(2018) João Henriques et al.   JOURNAL OF MOLECULAR BIOLOGY

Ab initio electron density determination directly from solution scattering data

(2018) Thomas D Grant   NATURE METHODS

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lessons from pressure denaturation of proteins

(2018) Julien Roche et al.   Journal of the Royal Society Interface

Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

(2018) Alejandro Estaña et al.   STRUCTURE

Bayesian inference of protein conformational ensembles from limited structural data

(2018) Wojciech Potrzebowski et al.   PLoS Computational Biology

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

(2017) Joshua A. Riback et al.   SCIENCE

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

(2017) Roman Shevchuk et al.   PLoS Computational Biology

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

(2017) Sergei Grudinin et al.   Acta Crystallographica Section D-Structural Biology

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

(2016) Alessandro Borgia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins

(2015) Alexey G. Kikhney et al.   FEBS LETTERS

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

(2015) João Henriques et al.   Journal of Chemical Theory and Computation

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

(2015) Christopher J. Knight et al.   NUCLEIC ACIDS RESEARCH

A posterioridetermination of the useful data range for small-angle scattering experiments on dilute monodisperse systems

(2015) Petr V. Konarev et al.   IUCrJ

Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering

(2015) Giancarlo Tria et al.   IUCrJ

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

(2014) Kyle A. Beauchamp et al.   BIOPHYSICAL JOURNAL

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

(2014) Po-chia Chen et al.   BIOPHYSICAL JOURNAL

The Effects of Thermal Disorder on the Solution-Scattering Profiles of Macromolecules

(2014) Peter B. Moore   BIOPHYSICAL JOURNAL

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

(2014) Ferruccio Palazzesi et al.   Journal of Chemical Theory and Computation

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

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

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

Characterization of disordered proteins with ENSEMBLE

(2012) Mickaël Krzeminski et al.   BIOINFORMATICS

Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

(2012) V. Ozenne et al.   BIOINFORMATICS

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering

(2011) Jouko Juhani Virtanen et al.   BIOPHYSICAL JOURNAL

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering

(2011) Pau Bernadó et al.   Molecular BioSystems

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

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

Modeling Intrinsically Disordered Proteins with Bayesian Statistics

(2010) Charles K. Fisher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

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

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

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

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

(2009) Malene Ringkjøbing Jensen et al.   STRUCTURE

Domain Conformation of Tau Protein Studied by Solution Small-Angle X-ray Scattering†

(2008) Efstratios Mylonas et al.   BIOCHEMISTRY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain

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