Bayesian ensemble refinement by replica simulations and reweighting

Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions

(2015) Fabrizio Marinelli et al.   BIOPHYSICAL JOURNAL

Hybrid methods for macromolecular structure determination: experiment with expectations

(2015) Gunnar F Schröder   CURRENT OPINION IN STRUCTURAL BIOLOGY

MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

(2015) Alexey B. Mantsyzov et al.   JOURNAL OF BIOMOLECULAR NMR

Designing Free Energy Surfaces That Match Experimental Data with Metadynamics

(2015) Andrew D. White et al.   Journal of Chemical Theory and Computation

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

(2015) Andrej Sali et al.   STRUCTURE

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

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

Uncertainty in integrative structural modeling

(2014) Dina Schneidman-Duhovny et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Time-averaged order parameter restraints in molecular dynamics simulations

(2014) Niels Hansen et al.   JOURNAL OF BIOMOLECULAR NMR

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

(2014) Andrew D. White et al.   Journal of Chemical Theory and Computation

Probabilistic Determination of Native State Ensembles of Proteins

(2014) Simon Olsson et al.   Journal of Chemical Theory and Computation

Statistical Mechanics of the Denatured State of a Protein Using Replica-Averaged Metadynamics

(2014) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings

(2014) M. Sanchez-Martinez et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Bayesian approach to inverse statistical mechanics

(2014) Michael Habeck   PHYSICAL REVIEW E

A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

(2014) Alexey B. Mantsyzov et al.   PROTEIN SCIENCE

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

Erratum: “Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle” [J. Chem. Phys. 138, 094112 (2013)]

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

(2013) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

Replica-Averaged Metadynamics

(2013) Carlo Camilloni et al.   Journal of Chemical Theory and Computation

Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies

(2013) Pilar Cossio et al.   JOURNAL OF STRUCTURAL BIOLOGY

Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

(2013) Konstantin Berlin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

On the Use of Experimental Observations to Bias Simulated Ensembles

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

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

Solution Structure of the ESCRT-I and -II Supercomplex: Implications for Membrane Budding and Scission

(2012) Evzen Boura et al.   STRUCTURE

Constructing ensembles for intrinsically disordered proteins

(2011) Charles K Fisher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins

(2011) Da-Wei Li et al.   Journal of Chemical Theory and Computation

Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations

(2011) Edina Rosta et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis of p38α regulation by hematopoietic tyrosine phosphatase

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

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

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

Modeling Intrinsically Disordered Proteins with Bayesian Statistics

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

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

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

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

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

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