Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Allosteric Inhibition of a Zinc-Sensing Transcriptional Repressor: Insights into the Arsenic Repressor (ArsR) Family

(2013) Gregory C. Campanello et al.   JOURNAL OF MOLECULAR BIOLOGY

N-Terminal Region of CusB Is Sufficient for Metal Binding and Metal Transfer with the Metallochaperone CusF

(2012) Tiffany D. Mealman et al.   BIOCHEMISTRY

Catalytic Mechanism of Aromatic Prenylation by NphB

(2012) Yue Yang et al.   BIOCHEMISTRY

Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery

(2012) Chul Won Lee et al.   BIOCHEMISTRY

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

(2012) Rinaldo W. Montalvao et al.   JOURNAL OF BIOMOLECULAR NMR

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Energetics of Zinc-Mediated Interactions in the Allosteric Pathways of Metal Sensor Proteins

(2012) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Wide-Open Flaps Are Key to Urease Activity

(2012) Benjamin P. Roberts et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

BioMe: biologically relevant metals

(2012) A. Tus et al.   NUCLEIC ACIDS RESEARCH

Accurate protein structure modeling using sparse NMR data and homologous structure information

(2012) J. M. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structural Basis for Polyadenosine-RNA Binding by Nab2 Zn Fingers and Its Function in mRNA Nuclear Export

(2012) Christoph Brockmann et al.   STRUCTURE

A Grid-enabled web portal for NMR structure refinement with AMBER

(2011) Ivano Bertini et al.   BIOINFORMATICS

Templated Construction of a Zn-Selective Protein Dimerization Motif

(2011) Eric N. Salgado et al.   INORGANIC CHEMISTRY

Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures

(2011) Jacopo Sgrignani et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

(2011) Alfonso De Simone et al.   Journal of Chemical Theory and Computation

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Electrostatic Polarization Is Crucial in Reproducing Cu(I) Interaction Energies and Hydration

(2011) Sergei Y. Ponomarev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insight into the Cation−π Interaction at the Metal Binding Site of the Copper Metallochaperone CusF

(2011) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simulations of Allosteric Motions in the Zinc Sensor CzrA

(2011) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into the Mechanistic Dichotomy of the Protein Farnesyltransferase Peptide Substrates CVIM and CVLS

(2011) Yue Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In Silico Elucidation of the Recognition Dynamics of Ubiquitin

(2011) Dong Long et al.   PLoS Computational Biology

Finding a Needle in the Haystack: Computational Modeling of Mg2+Binding in the Active Site of Protein Farnesyltransferase

(2010) Yue Yang et al.   BIOCHEMISTRY

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

(2010) Johnny C. Wu et al.   Journal of Chemical Theory and Computation

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems

(2010) Fu Lin et al.   Journal of Chemical Theory and Computation

A Transferable Nonbonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

(2010) Ruibo Wu et al.   Journal of Chemical Theory and Computation

QM/MM X-ray refinement of zinc metalloenzymes

(2010) Xue Li et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Impact of Mutation on Proton Transfer Reactions in Ketosteroid Isomerase: Insights from Molecular Dynamics Simulations

(2010) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

(2010) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of Metal Selectivity in Templated Protein Interfaces

(2010) Jeffrey D. Brodin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose)

(2010) Sebastian Eustermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

(2010) S. Raman et al.   SCIENCE

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

(2010) Paul Robustelli et al.   STRUCTURE

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

(2009) Dhruva K. Chakravorty et al.   BIOCHEMISTRY

Coordination Chemistry of Bacterial Metal Transport and Sensing

(2009) Zhen Ma et al.   CHEMICAL REVIEWS

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

Energetics of Allosteric Negative Coupling in the Zinc SensorS. aureusCzrA

(2009) Nicholas E. Grossoehme et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs

(2009) Andrew C. Stelzer et al.   METHODS

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Density functional theory for transition metals and transition metal chemistry

(2009) Christopher J. Cramer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Metal templated design of protein interfaces

(2009) E. N. Salgado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

(2009) A. I. Arunkumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular modelling for transition metal complexes: Dealing with d-electron effects

(2008) Robert J. Deeth et al.   COORDINATION CHEMISTRY REVIEWS

Implementation of Umbrella Integration within the Framework of the Empirical Valence Bond Approach

(2008) Dhruva K. Chakravorty et al.   Journal of Chemical Theory and Computation

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

(2008) Nicole M. Settergren et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How do bacterial cells ensure that metalloproteins get the correct metal?

(2008) Kevin J. Waldron et al.   NATURE REVIEWS MICROBIOLOGY

Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study

(2008) Theresa A. Ramelot et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Solution NMR Structure of a Designed Metalloprotein and Complementary Molecular Dynamics Refinement

(2008) Jennifer R. Calhoun et al.   STRUCTURE

Metal-Coupled Folding of Cys2His2Zinc-Finger

(2007) Wenfei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY