Synergistic Applications of MD and NMR for the Study of Biological Systems

Nuclear Magnetic Resonance Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Time Scales

(2011) Loïc Salmon et al.   BIOCHEMISTRY

Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations

(2011) Tod D. Romo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Protein–protein HADDocking using exclusively pseudocontact shifts

(2011) Christophe Schmitz et al.   JOURNAL OF BIOMOLECULAR NMR

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

A practical guide to protein dynamics from 15N spin relaxation in solution

(2011) Sébastien Morin   PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

TEM-1 Backbone Dynamics—Insights from Combined Molecular Dynamics and Nuclear Magnetic Resonance

(2010) Olivier Fisette et al.   BIOPHYSICAL JOURNAL

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations

(2010) Samuel Genheden et al.   Journal of Chemical Theory and Computation

Structural NMR of protein oligomers using hybrid methods

(2010) Xu. Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Defining Conformational Ensembles of Intrinsically Disordered and Partially Folded Proteins Directly from Chemical Shifts

(2010) Malene Ringkjøbing Jensen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational Space of Flexible Biological Macromolecules from Average Data

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

Interpreting protein chemical shift data

(2010) David S. Wishart   PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

(2010) S. Raman et al.   SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Dynameomics: A Comprehensive Database of Protein Dynamics

(2010) Marc W. van der Kamp et al.   STRUCTURE

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

(2009) Lauren Wickstrom et al.   BIOPHYSICAL JOURNAL

The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids

(2009) Bertil Halle   JOURNAL OF CHEMICAL PHYSICS

Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States

(2009) Debabani Ganguly et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

(2009) Joseph A. Marsh et al.   JOURNAL OF MOLECULAR BIOLOGY

Referencing Strategy for the Direct Comparison of Nuclear Magnetic Resonance and Molecular Dynamics Motional Parameters in RNA

(2009) Catherine Musselman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Certification of Molecular Dynamics Trajectories with NMR Chemical Shifts

(2009) Da-Wei Li et al.   Journal of Physical Chemistry Letters

Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data

(2009) Srivatsan Raman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational averaging in structural biology: issues, challenges and computational solutions

(2009) Daniela Kruschel et al.   Molecular BioSystems

NMR spectroscopy brings invisible protein states into focus

(2009) Andrew J Baldwin et al.   Nature Chemical Biology

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

Observing biological dynamics at atomic resolution using NMR

(2009) Anthony K. Mittermaier et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural Polymorphism of 441-Residue Tau at Single Residue Resolution

(2009) Marco D Mukrasch et al.   PLOS BIOLOGY

Starting Structure Dependence of NMR Order Parameters Derived from MD Simulations: Implications for Judging Force-Field Quality

(2008) Alrun N. Koller et al.   BIOPHYSICAL JOURNAL

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

United we stand: combining structural methods

(2008) Nathan P Cowieson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

De novo protein structure generation from incomplete chemical shift assignments

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

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Multifaceted Approach to the Interpretation of NMR Order Parameters:  A Case Study of a Dynamic α-Helix†

(2008) Eric Johnson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Benchmarking Implicit Solvent Folding Simulations of the Amyloid β(10−35) Fragment†

(2008) Andrew Kent et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of the Aβ21–30Peptide from the Interplay of NMR Experiments and Molecular Simulations

(2008) Nicolas L. Fawzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

(2008) Jan Ferner et al.   NUCLEIC ACIDS RESEARCH

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

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

(2008) D. A.C. Beck et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Evaluating Rotational Diffusion from Protein MD Simulations†

(2007) Vance Wong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

(2007) Nikola Trbovic et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS