Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

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

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

(2013) Wouter Boomsma et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Inference of Structure Ensembles of Flexible Biomolecules from Sparse, Averaged Data

(2013) Simon Olsson et al.   PLoS One

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks

(2012) Martin Paluszewski et al.   BMC BIOINFORMATICS

On the Use of Experimental Observations to Bias Simulated Ensembles

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

Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts

(2012) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

(2012) Antonio Rosato et al.   STRUCTURE

Using Enhanced Sampling and Structural Restraints to Refine Atomic Structures into Low-Resolution Electron Microscopy Maps

(2012) Harish Vashisth et al.   STRUCTURE

Proteins at Work

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

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

Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

(2010) Paul Robustelli et al.   STRUCTURE

Folding of Small Proteins by Monte Carlo Simulations with Chemical Shift Restraints without the Use of Molecular Fragment Replacement or Structural Homology

(2009) Paul Robustelli et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An effective all-atom potential for proteins

(2009) Anders Irbäck et al.   BMC Biophysics

De novo protein structure generation from incomplete chemical shift assignments

(2008) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

A generative, probabilistic model of local protein structure

(2008) Wouter Boomsma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent blind protein structure generation from NMR chemical shift data

(2008) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of Protein Structures in the Solid State from NMR Chemical Shifts

(2008) Paul Robustelli et al.   STRUCTURE

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

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