Characterizing RNA ensembles from NMR data with kinematic models

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

(2014) Prashant S. Emani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein-guided RNA dynamics during early ribosome assembly

(2014) Hajin Kim et al.   NATURE

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

(2014) Parin Sripakdeevong et al.   NATURE METHODS

From a structural average to the conformational ensemble of a DNA bulge

(2014) X. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

(2014) R. B. Fenwick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral–Host Interactions That Control HIV-1 Transcriptional Elongation

(2013) Huasong Lu et al.   CHEMICAL REVIEWS

Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics

(2013) Aaron T. Frank et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Automated identification of functional dynamic contact networks from X-ray crystallography

(2013) Henry van den Bedem et al.   NATURE METHODS

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

(2013) Samuel Coulbourn Flores   NUCLEIC ACIDS RESEARCH

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

Determining RNA three-dimensional structures using low-resolution data

(2012) Marc Parisien et al.   JOURNAL OF STRUCTURAL BIOLOGY

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

Modeling and design by hierarchical natural moves

(2012) A. Y. L. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Landscape of RNA Dynamics with NMR Spectroscopy

(2011) Jörg Rinnenthal et al.   ACCOUNTS OF CHEMICAL RESEARCH

Computational approaches to RNA structure prediction, analysis, and design

(2011) Christian Laing et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dual functional RNA nanoparticles containing phi29 motor pRNA and anti-gp120 aptamer for cell-type specific delivery and HIV-1 Inhibition

(2011) Jiehua Zhou et al.   METHODS

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

ModeRNA: a tool for comparative modeling of RNA 3D structure

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Sampling-based exploration of folded state of a protein under kinematic and geometric constraints

(2011) Peggy Yao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Crystal structure of HIV-1 Tat complexed with human P-TEFb

(2010) Tahir H. Tahirov et al.   NATURE

The emerging field of RNA nanotechnology

(2010) Peixuan Guo   Nature Nanotechnology

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

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

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

Characterizing Complex Dynamics in the Transactivation Response Element Apical Loop and Motional Correlations with the Bulge by NMR, Molecular Dynamics, and Mutagenesis

(2008) Elizabeth A. Dethoff et al.   BIOPHYSICAL JOURNAL

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops

(2008) P. Yao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

NMR: prediction of molecular alignment from structure using the PALES software

(2008) Markus Zweckstetter   Nature Protocols

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