Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

(2014) Anthony M. Mustoe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graph-based sampling for approximating global helical topologies of RNA

(2014) N. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Unusual Topological Structure of the HIV-1 Rev Response Element

(2013) Xianyang Fang et al.   CELL

Sequence-Dependent Base-Stacking Stabilities Guide tRNA Folding Energy Landscapes

(2013) Rongzhong Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crowders Perturb the Entropy of RNA Energy Landscapes to Favor Folding

(2013) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperative Tertiary Interaction Network Guides RNA Folding

(2012) Reza Behrouzi et al.   CELL

Automated prediction of three-way junction topological families in RNA secondary structures

(2012) Alexis Lamiable et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Modeling nucleic acids

(2012) Adelene YL Sim et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures

(2012) Eda Koculi et al.   NUCLEIC ACIDS RESEARCH

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

(2011) Maximillian H Bailor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints

(2011) Matthew G. Seetin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

(2011) Natalia A. Denesyuk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

3D maps of RNA interhelical junctions

(2011) Maximillian H Bailor et al.   Nature Protocols

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

(2011) Anthony M. Mustoe et al.   NUCLEIC ACIDS RESEARCH

Clustering to identify RNA conformations constrained by secondary structure

(2011) Adelene Y. L. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Structure of transfer RNAs: similarity and variability

(2011) Richard Giegé et al.   Wiley Interdisciplinary Reviews-RNA

Compact Intermediates in RNA Folding

(2010) Sarah A. Woodson   Annual Review of Biophysics

Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

(2010) Christopher A. Lavender et al.   BIOCHEMISTRY

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

(2010) Mariusz Popenda et al.   BMC BIOINFORMATICS

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

Folding and Finding RNA Secondary Structure

(2010) D. H. Mathews et al.   Cold Spring Harbor Perspectives in Biology

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Experimental and computational determination of tRNA dynamics

(2009) Rebecca W. Alexander et al.   FEBS LETTERS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Analysis of Four-Way Junctions in RNA Structures

(2009) Christian Laing et al.   JOURNAL OF MOLECULAR BIOLOGY

Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions

(2009) Christian Laing et al.   JOURNAL OF MOLECULAR BIOLOGY

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

(2009) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) M. A. Jonikas et al.   RNA

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

(2009) V. B. Chu et al.   RNA

Structural Principles From Large RNAs

(2008) Stephen R. Holbrook   Annual Review of Biophysics

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

A repulsive field: advances in the electrostatics of the ion atmosphere

(2008) Vincent B Chu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Direct Measurement of Tertiary Contact Cooperativity in RNA Folding

(2008) Bernie D. Sattin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH