4.7 Article

A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

Hierarchy of RNA Functional Dynamics

Anthony M. Mustoe et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Review Biochemistry & Molecular Biology

Understanding Nucleic Acid-Ion Interactions

Jan Lipfert et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Review Physics, Multidisciplinary

RNA structure prediction: Progress and perspective

Shi Ya-Zhou et al.

CHINESE PHYSICS B (2014)

Article Chemistry, Physical

A nucleotide-level coarse-grained model of RNA

Petr Sulc et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

Combining temperature and force to study folding of an RNA hairpin

William Stephenson et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)

Review Biophysics

Coarse-Graining Methods for Computational Biology

Marissa G. Saunders et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 42 (2013)

Article Biochemistry & Molecular Biology

Role of Ion Valence in the Submillisecond Collapse and Folding of a Small RNA Domain

Suzette A. Pabit et al.

BIOCHEMISTRY (2013)

Review Biochemistry & Molecular Biology

Folding of RNA Tertiary Structure: Linkages Between Backbone Phosphates, Ions, and Water

David E. Draper

BIOPOLYMERS (2013)

Article Biochemistry & Molecular Biology

Salt contribution to the flexibility of single-stranded nucleic acid offinite length

Feng-Hua Wang et al.

BIOPOLYMERS (2013)

Article Chemistry, Physical

Perspective: Reaches of chemical physics in biology

Martin Gruebele et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Perspective: Coarse-grained models for biomolecular systems

W. G. Noid

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field

Filip Leonarski et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Coarse-Grained Simulations of RNA and DNA Duplexes

Tristan Cragnolini et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Physical

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

Zhen Xia et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Physical

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

Natalia A. Denesyuk et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Multidisciplinary Sciences

Predicting Helical Topologies in RNA Junctions as Tree Graphs

Christian Laing et al.

PLOS ONE (2013)

Editorial Material Multidisciplinary Sciences

RNA does the folding dance of twist, turn, stack

Kathleen B. Hall

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Yangyu Huang et al.

SCIENTIFIC REPORTS (2013)

Article Biophysics

Ion-Mediated RNA Structural Collapse: Effect of Spatial Confinement

Zhi-Jie Tan et al.

BIOPHYSICAL JOURNAL (2012)

Article Chemistry, Physical

Kinetic analysis of the effects of target structure on siRNA efficiency

Jiawen Chen et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

Article Chemistry, Physical

Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching

Naoto Hori et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Biochemistry & Molecular Biology

Discrete RNA Libraries from Pseudo-Torsional Space

Elisabeth Humphris-Narayanan et al.

JOURNAL OF MOLECULAR BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Determining RNA three-dimensional structures using low-resolution data

Marc Parisien et al.

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Article Chemistry, Multidisciplinary

Kinetic Mechanism of Conformational Switch between Bistable RNA Hairpins

Xiaojun Xu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemical Research Methods

Three-dimensional RNA structure refinement by hydroxyl radical probing

Feng Ding et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Automated 3D structure composition for large RNAs

Mariusz Popenda et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Physics, Fluids & Plasmas

RNA fragment modeling with a nucleobase discrete-state model

Jian Zhang et al.

PHYSICAL REVIEW E (2012)

Article Multidisciplinary Sciences

Modeling and design by hierarchical natural moves

Adelene Y. L. Sim et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Improved prediction of RNA tertiary structure with insights into native state dynamics

John Paul Bida et al.

Article Biochemistry & Molecular Biology

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

Jose Almeida Cruz et al.

Article Multidisciplinary Sciences

Automated and fast building of three-dimensional RNA structures

Yunjie Zhao et al.

SCIENTIFIC REPORTS (2012)

Review Chemistry, Multidisciplinary

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

Samuel E. Butcher et al.

ACCOUNTS OF CHEMICAL RESEARCH (2011)

Review Chemistry, Physical

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

Juan J. de Pablo

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 62 (2011)

Article Biophysics

Salt Contribution to RNA Tertiary Structure Folding Stability

Zhi-Jie Tan et al.

BIOPHYSICAL JOURNAL (2011)

Article Biochemistry & Molecular Biology

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

Maximillian H. Bailor et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Computational approaches to RNA structure prediction, analysis, and design

Christian Laing et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure

Yunjie Zhao et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2011)

Article Chemistry, Multidisciplinary

Automated RNA Tertiary Structure Prediction from Secondary Structure and Low-Resolution Restraints

Matthew G. Seetin et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

RNA and protein 3D structure modeling: similarities and differences

Kristian Rother et al.

JOURNAL OF MOLECULAR MODELING (2011)

Article Chemistry, Physical

Physics-Based De Novo Prediction of RNA 3D Structures

Song Cao et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Chemistry, Multidisciplinary

Atomistic Analysis of Pseudoknotted RNA Unfolding

Yujie Zhang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Chemistry, Multidisciplinary

Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations

Shi Biyun et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Biochemistry & Molecular Biology

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

Magdalena Rother et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

Fabrice Jossinet et al.

BIOINFORMATICS (2010)

Article Biophysics

Predicting Secondary Structural Folding Kinetics for Nucleic Acids

Peinan Zhao et al.

BIOPHYSICAL JOURNAL (2010)

Article Biophysics

Predicting Ion Binding Properties for RNA Tertiary Structures

Zhi-Jie Tan et al.

BIOPHYSICAL JOURNAL (2010)

Article Chemistry, Physical

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

Zhen Xia et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Physical

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

Samuela Pasquali et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Review Physics, Condensed Matter

Computational approaches to 3D modeling of RNA

Christian Laing et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2010)

Article Biochemical Research Methods

Atomic accuracy in predicting and designing noncanonical RNA structure

Rhiju Das et al.

NATURE METHODS (2010)

Article Physics, Fluids & Plasmas

Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials

Oscar Taxilaga-Zetina et al.

PHYSICAL REVIEW E (2010)

Article Biochemistry & Molecular Biology

Turning limited experimental information into 3D models of RNA

Samuel Coulbourn Flores et al.

Article Biochemistry & Molecular Biology

On the significance of an RNA tertiary structure prediction

Christine E. Hajdin et al.

Article Biochemistry & Molecular Biology

Coarse-graining RNA nanostructures for molecular dynamics simulations

Maxim Paliy et al.

PHYSICAL BIOLOGY (2010)

Article Biochemical Research Methods

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

Magdalena A. Jonikas et al.

BIOINFORMATICS (2009)

Article Chemistry, Multidisciplinary

Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

Costin M. Gherghe et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Biochemistry & Molecular Biology

Conformational analysis of nucleic acids revisited: Curves

R. Lavery et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

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

Magdalena A. Jonikas et al.

Article Biochemistry & Molecular Biology

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

Marc Parisien et al.

Article Biochemical Research Methods

A Probabilistic Model of RNA Conformational Space

Jes Frellsen et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Review Biochemistry & Molecular Biology

How RNA unfolds and refolds

Pan T. X. Li et al.

ANNUAL REVIEW OF BIOCHEMISTRY (2008)

Review Biophysics

RNA folding: Conformational statistics, folding kinetics, and ion electrostatics

Shi-Jie Chen

ANNUAL REVIEW OF BIOPHYSICS (2008)

Article Biochemical Research Methods

iFoldRNA: three-dimensional RNA structure prediction and folding

Shantanu Sharma et al.

BIOINFORMATICS (2008)

Article Biophysics

Salt dependence of nucleic acid hairpin stability

Zhi-Jie Tan et al.

BIOPHYSICAL JOURNAL (2008)

Article Biochemistry & Molecular Biology

RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA

Hugo M. Martinez et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2008)

Article Chemistry, Physical

Theory of competitive counterion adsorption on flexible polyelectrolytes: Divalent salts

Arindam Kundagrami et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Multidisciplinary

Tertiary interactions determine the accuracy of RNA folding

Seema Chauhan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Multidisciplinary Sciences

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

Marc Parisien et al.

NATURE (2008)

Article Multidisciplinary Sciences

Structural inference of native and partially folded RNA by high-throughput contact mapping

Rhiju Dast et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Automated de novo prediction of native-like RNA tertiary structures

Rhiju Das et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Riboswitches:: small-molecule recognition by gene regulatory RNAs

Thomas E. Edwards et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Review Biophysics

RNA helix stability in mixed Na+/Mg2+ solution

Zhi-Jie Tan et al.

BIOPHYSICAL JOURNAL (2007)

Article Biochemistry & Molecular Biology

Bridging the gap in RNA structure prediction

Bruce A. Shapiro et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Tertiary structure of an RNA pseudoknot is stabilized by diffuse Mg2+ ions

Ana Maria Soto et al.

BIOCHEMISTRY (2007)

Article Chemistry, Physical

Coarse-grained model of coil-to-helix kinetics demonstrates the importance of multiple nucleation sites in helix folding

Alan E. van Giessen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)

Article Chemistry, Physical

YUP: A molecular simulation program for coarse-grained and multiscaled models

Robert K. Z. Tan et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)

Article Biochemistry & Molecular Biology

Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops

CJ Vecenie et al.

BIOCHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Predicting RNA pseudoknot folding thermodynamics

Song Cao et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Predicting RNA folding thermodynamics with a reduced chain representation model

S Cao et al.

Article Multidisciplinary Sciences

Mechanical unfolding of RNA hairpins

C Hyeon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Review Biochemistry & Molecular Biology

Metal ions and RNA folding: a highly charged topic with a dynamic future

SA Woodson

CURRENT OPINION IN CHEMICAL BIOLOGY (2005)

Article Chemistry, Physical

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

ZJ Tan et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Biochemistry & Molecular Biology

Stability of RNA hairpin loops closed by AU base pairs

CJ Vecenie et al.

BIOCHEMISTRY (2004)

Article Chemistry, Physical

Theory of counter-ion condensation on flexible polyelectrolytes: Adsorption mechanism

M Muthukumar

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biochemistry & Molecular Biology

A structural model for the assembly of the 30 S subunit of the ribosome

SM Stagg et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Review Multidisciplinary Sciences

RNA interference

GJ Hannon

NATURE (2002)

Article Multidisciplinary Sciences

RNA hairpin-folding kinetics

WB Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot

PL Nixon et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)