Automated and fast building of three-dimensional RNA structures (Q36316650)

13 August 2017

Automated and fast building of three-dimensional RNA structures (English)

1 reference

13 August 2017

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Yunjie Zhao

1

1 reference

13 August 2017

Yangyu Huang

2

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13 August 2017

Zhou Gong

3

1 reference

13 August 2017

Yanjie Wang

4

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13 August 2017

Jianfen Man

5

1 reference

13 August 2017

Yi Xiao

6

1 reference

13 August 2017

language of work or name

English

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publication date

15 October 2012

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13 August 2017

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13 August 2017

2

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13 August 2017

734

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Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported

13 August 2017

start time

15 October 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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exact match

https://scigraph.springernature.com/pub.10.1038/srep00734

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cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Computational approaches to RNA structure prediction, analysis, and design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Atomic accuracy in predicting and designing noncanonical RNA structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

CD-HIT Suite: a web server for clustering and comparing biological sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

A probabilistic model of RNA conformational space

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

iFoldRNA: three-dimensional RNA structure prediction and folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Automated de novo prediction of native-like RNA tertiary structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Bridging the gap in RNA structure prediction.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

SCOR: a Structural Classification of RNA database

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Convergent solutions to binding at a protein-protein interface

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

MANIP: an interactive tool for modelling RNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

VMD: visual molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

RNAshapes: an integrated RNA analysis package based on abstract shapes.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Quantitative analysis of nucleic acid three-dimensional structures.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3471093

Improvements of the hierarchical approach for predicting RNA tertiary structure

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23071898

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

RNA stability under different combinations of amber force fields and solvation models

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23071898

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP00734

1 reference

13 August 2017

1 reference

13 August 2017

1 reference