Computational modeling of RNA 3D structures, with the aid of experimental restraints

Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR

(2013) Edis Dzananovic et al.   JOURNAL OF STRUCTURAL BIOLOGY

RNA Bricks—a database of RNA 3D motifs and their interactions

(2013) Grzegorz Chojnowski et al.   NUCLEIC ACIDS RESEARCH

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2013) Tomasz Puton et al.   NUCLEIC ACIDS RESEARCH

T box RNA decodes both the information content and geometry of tRNA to affect gene expression

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

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

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

(2013) James D. Stephenson et al.   STRUCTURE

Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution

(2012) David A. Jacques et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Molecular recognition and function of riboswitches

(2012) Alexander Serganov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

(2012) Hugo M. Martinez et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

A toolkit and benchmark study for FRET-restrained high-precision structural modeling

(2012) Stanislav Kalinin et al.   NATURE METHODS

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids

(2012) Søren Preus et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

(2012) Kourosh Zarringhalam et al.   PLoS One

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

(2012) J. A. Cruz et al.   RNA

From crystal to structure with CCP4

(2011) Kevin Cowtan et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

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

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Sharing and archiving nucleic acid structure mapping data

(2011) P. Rocca-Serra et al.   RNA

Visualizing large RNA molecules in solution

(2011) A. Gopal et al.   RNA

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

FILTREST3D: discrimination of structural models using restraints from experimental data

(2010) Michal J. Gajda et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

RNA Structure Determination Using SAXS Data

(2010) Sichun Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational approaches to 3D modeling of RNA

(2010) Christian Laing et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Improving the accuracy of predicting secondary structure for aligned RNA sequences

(2010) Michiaki Hamada et al.   NUCLEIC ACIDS RESEARCH

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Multiscale Modeling of Proteins

(2009) Valentina Tozzini   ACCOUNTS OF CHEMICAL RESEARCH

A New Computational Approach for Mechanical Folding Kinetics of RNA Hairpins

(2009) Song Cao et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

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

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

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

(2009) M. A. Jonikas et al.   RNA

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

A fast structural multiple alignment method for long RNA sequences

(2008) Yasuo Tabei et al.   BMC BIOINFORMATICS

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

(2008) Marc Parisien et al.   NATURE

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

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

(2008) R. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MS3D structural elucidation of the HIV-1 packaging signal

(2008) E. T. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annotation of tertiary interactions in RNA structures reveals variations and correlations

(2008) Y. Xin et al.   RNA

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA