RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction (Q35853409)

10 August 2017

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

1 reference

10 August 2017

José Almeida Cruz

1

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Christopher A Lavender

Christopher A Lavender

12

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Alexander Serganov

Alexander Serganov

24

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Neocles Leontis

Neocles B Leontis

32

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Shi-Jie Chen

Shi-Jie Chen

5

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Feng Ding

Feng Ding

8

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Rhiju Das

Rhiju Das

7

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Nikolay V. Dokholyan

Nikolay V Dokholyan

9

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Anna Philips

Anna Philips

17

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Janusz Bujnicki

4

Janusz M Bujnicki

1 reference

10 August 2017

33

Eric Westhof

1 reference

10 August 2017

22

Kristian Rother

1 reference

10 August 2017

14

François Major

1 reference

10 August 2017

Marc-Frédérick Blanchet

2

1 reference

10 August 2017

Michal Boniecki

3

1 reference

10 August 2017

Song Cao

6

1 reference

10 August 2017

Samuel Coulbourn Flores

10

1 reference

10 August 2017

Lili Huang

11

1 reference

10 August 2017

Véronique Lisi

13

1 reference

10 August 2017

Katarzyna Mikolajczak

15

1 reference

10 August 2017

Dinshaw J Patel

16

1 reference

10 August 2017

Tomasz Puton

18

1 reference

10 August 2017

John Santalucia

19

1 reference

10 August 2017

Fredrick Sijenyi

20

1 reference

10 August 2017

Thomas Hermann

21

1 reference

10 August 2017

Magdalena Rother

23

1 reference

10 August 2017

Marcin Skorupski

25

1 reference

10 August 2017

Tomasz Soltysinski

26

1 reference

10 August 2017

Parin Sripakdeevong

27

1 reference

10 August 2017

Irina Tuszynska

28

1 reference

10 August 2017

Kevin M Weeks

29

1 reference

10 August 2017

Christina Waldsich

30

1 reference

10 August 2017

Michael Wildauer

31

1 reference

10 August 2017

language of work or name

English

0 references

publication date

23 February 2012

1 reference

10 August 2017

1 reference

10 August 2017

18

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10 August 2017

4

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10 August 2017

610-625

1 reference

Simbody: multibody dynamics for biomedical research

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Fast flexible modeling of RNA structure using internal coordinates.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Self-assembling RNA square

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

RNA and protein 3D structure modeling: similarities and differences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Turning limited experimental information into 3D models of RNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

On the significance of an RNA tertiary structure prediction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

RNAstructure: software for RNA secondary structure prediction and analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Atomic accuracy in predicting and designing noncanonical RNA structure

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Predicting RNA structure by multiple template homology modeling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

VARNA: Interactive drawing and editing of the RNA secondary structure

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Rfam: updates to the RNA families database

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Ab initio folding of proteins with all-atom discrete molecular dynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Macromolecular modeling with rosetta

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Structure of hepatitis C virus IRES subdomain IIa

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

11 July 2018

The Monte Carlo method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

High-resolution structure prediction and the crystallographic phase problem

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Predicting RNA pseudoknot folding thermodynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Rigorous performance evaluation in protein structure modelling and implications for computational biology.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Scoring function for automated assessment of protein structure template quality

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

A glycine-dependent riboswitch that uses cooperative binding to control gene expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Protein fragment reconstruction using various modeling techniques

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

PDB file parser and structure class implemented in Python

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

RNA backbone is rotameric

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Tools for the automatic identification and classification of RNA base pairs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Mfold web server for nucleic acid folding and hybridization prediction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

LGA: A method for finding 3D similarities in protein structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

The non-Watson-Crick base pairs and their associated isostericity matrices

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Reliability of assessment of protein structure prediction methods.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Geometric nomenclature and classification of RNA base pairs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

11 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Improved Estimation of Secondary Structure in Ribonucleic Acids

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Sequence-based identification of 3D structural modules in RNA with RMDetect

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Predicting RNA folding thermodynamics with a reduced chain representation model.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

Quantitative analysis of nucleic acid three-dimensional structures.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3312550

A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22361291

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.031054.111

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

22361291

1 reference