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List of works by Shi-Jie Chen

A Method to Predict the 3D Structure of an RNA Scaffold

scientific article published on January 2015

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

scientific article published on January 2016

A New Method to Predict Ion Effects in RNA Folding.

scientific article published in January 2017

A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable.

scientific article

A new computational approach for mechanical folding kinetics of RNA hairpins.

scientific article published on May 2009

Coarse-grained prediction of RNA loop structures.

scientific article

Computing the conformational entropy for RNA folds.

scientific article published on June 2010

Cotranscriptional folding kinetics of ribonucleic acid secondary structures

scientific article published on December 2011

Designing a Polycationic Probe for Simultaneous Enrichment and Detection of MicroRNAs in a Nanopore ⬇️

scientific article published on April 10, 2013

Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte.

scientific article published on January 2005

Electrostatic free energy landscapes for DNA helix bending

scientific article published on 11 January 2008

Electrostatic free energy landscapes for nucleic acid helix assembly

scientific article published on December 2006

Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis.

scientific article

Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states

scientific article

Exploring the electrostatic energy landscape for tetraloop-receptor docking.

scientific article published on 10 December 2013

Folding kinetics for the conformational switch between alternative RNA structures

scientific article published on October 2010

Folding thermodynamics of pseudoknotted chain conformations.

scientific article published on April 2006

Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes

scientific article published on 21 December 2005

Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.

scientific article published on 20 December 2017

In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs

scientific article

Ion-mediated RNA structural collapse: effect of spatial confinement.

scientific article

Ion-mediated nucleic acid helix-helix interactions

scientific article

IsRNA1: <i>De Novo</i> Prediction and Blind Screening of RNA 3D Structures

scientific article published on 09 February 2021

IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.

scientific article published on 2 March 2018

Kinetic mechanism of conformational switch between bistable RNA hairpins.

scientific article published on 19 July 2012

Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding

scientific article published on 08 February 2022

MCTBI: a web server for predicting metal ion effects in RNA structures

scientific article published on 27 April 2017

Many-body effect in ion binding to RNA.

scientific article published on August 2014

Master equation approach to finding the rate-limiting steps in biopolymer folding.

scientific article published on February 2003

Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel.

scientific article published on 23 November 2015

Minimizing off-target effects in CRISPR-Cas9 genome editing

scientific article published on 17 July 2019

Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations

scientific article published on 17 June 2016

NMR study of RNA structures in the 3´-end of the Hepatitis C Virus genome.

scientific article

Nanopore electric snapshots of an RNA tertiary folding pathway.

scientific article

Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length

scientific article

Physics-based de novo prediction of RNA 3D structures.

scientific article published on 17 March 2011

Predicting Cotranscriptional Folding Kinetics For Riboswitch

scientific article published on 19 July 2018

Predicting Ion Effects in an RNA Conformational Equilibrium.

scientific article published on 5 August 2017

Predicting Molecular Crowding Effects in Ion-RNA Interactions

scientific article

Predicting RNA Structure with Vfold

scientific article published in January 2017

Predicting RNA folding thermodynamics with a reduced chain representation model.

scientific article published on 26 October 2005

Predicting ion-nucleic acid interactions by energy landscape-guided sampling

scientific article published on 30 April 2012

Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity.

scientific article

Predicting ribosomal frameshifting efficiency.

scientific article published on 11 March 2008

Predicting secondary structural folding kinetics for nucleic acids.

scientific article

Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing

scientific article

Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

scientific article published on 23 February 2009

Preface

Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices ⬇️

scientific article published on June 7, 2013

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis

scientific article published on 27 April 2018

RLDOCK: A New Method for Predicting RNA-Ligand Interactions

scientific article published on 23 October 2020

RNA folding energy landscapes.

scientific article

RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

scientific article published on January 2008

RNA helix stability in mixed Na+/Mg2+ solution

scientific article published on 26 February 2007

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

scientific article published on 16 April 2015

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

scientific article

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

scientific article published on 23 February 2012

Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.

scientific article

Salt-dependent folding energy landscape of RNA three-way junction

scientific article

Statistical thermodynamics for chain molecules with simple RNA tertiary contacts.

scientific article published on March 2005

Structural computational modeling of RNA aptamers

scientific article

TBI server: a web server for predicting ion effects in RNA folding

scientific article published on 23 March 2015

Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules

scientific article

Understanding the kinetic mechanism of RNA single base pair formation

scientific article

Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design

scientific article published on 15 April 2019

Vfold: a web server for RNA structure and folding thermodynamics prediction

scientific article

VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability

scientific article

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