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

Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations

(2019) Po-chia Chen 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

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

Biological small-angle neutron scattering: recent results and development

(2018) Emilie Mahieu et al.   Acta Crystallographica Section D-Structural Biology

Bayesian inference of protein conformational ensembles from limited structural data

(2018) Wojciech Potrzebowski et al.   PLoS Computational Biology

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

(2018) Andrej Berg et al.   PLoS Computational Biology

Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering

(2017) Søren Roi Midtgaard et al.   FEBS Journal

GenApp: Extensible tool for rapid generation of web and native GUI applications

(2017) Alexey Savelyev et al.   Future Generation Computer Systems-The International Journal of eScience

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

(2017) Grzegorz Nawrocki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Excessive aggregation of membrane proteins in the Martini model

(2017) Matti Javanainen et al.   PLoS One

Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures

(2016) O. Dunne et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems

(2016) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins

(2016) David H. Brookes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

(2016) Dina Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Bayesian inference of protein ensembles from SAXS data

(2016) L. D. Antonov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A critical assessment of methods to recover information from averaged data

(2016) Enrico Ravera et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Efficient segmental isotope labeling of multi-domain proteins using Sortase A

(2015) Lee Freiburger et al.   JOURNAL OF BIOMOLECULAR NMR

Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α

(2015) Elise Delaforge et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2015) Petr V. Konarev et al.   IUCrJ

Insights into Domain–Domain Motions in Proteins and RNA from Solution NMR

(2014) Enrico Ravera et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

Transient Electrostatic Interactions Dominate the Conformational Equilibrium Sampled by Multidomain Splicing Factor U2AF65: A Combined NMR and SAXS Study

(2014) Jie-rong Huang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

(2014) Iren Wang et al.   NUCLEIC ACIDS RESEARCH

Quantification of the information in small-angle scattering data

(2014) Martin Cramer Pedersen et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

(2013) Austin C. Stark et al.   Journal of Chemical Theory and Computation

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

BayesApp: a web site for indirect transformation of small-angle scattering data

(2012) Steen Hansen   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Structural basis of p38α regulation by hematopoietic tyrosine phosphatase

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

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

Protein stability, flexibility and function

(2010) Kaare Teilum et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Conformational Space of Flexible Biological Macromolecules from Average Data

(2010) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins

(2007) Anders B. Norgaard et al.   BIOPHYSICAL JOURNAL