(Q37460103)

20 August 2017

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

1 reference

20 August 2017

3

Russ B Altman

1 reference

20 August 2017

Magdalena A Jonikas

1

1 reference

PMCID

2788923

20 August 2017

Randall J Radmer

series ordinal

2

1 reference

PMCID

2788923

20 August 2017

language of work or name

English

0 references

publication date

7 October 2009

1 reference

20 August 2017

8

1 reference

based on heuristic

inferred from page(s)

published in

Bioinformatics

1 reference

20 August 2017

25

1 reference

20 August 2017

24

1 reference

20 August 2017

3259-3266

1 reference

YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Structural and electrostatic characterization of pariacoto virus: implications for viral assembly

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

iFoldRNA: three-dimensional RNA structure prediction and folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Automated de novo prediction of native-like RNA tertiary structures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Structural evidence for a two-metal-ion mechanism of group I intron splicing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Crystal structure of a phage Twort group I ribozyme-product complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Genetic control by a metabolite binding mRNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Structural insights into group II intron catalysis and branch-site selection

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Crystal structure of the ribosome at 5.5 A resolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

MANIP: an interactive tool for modelling RNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Crystal structure of a group I ribozyme domain: principles of RNA packing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Detailed molecular model for transfer ribonucleic acid

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Ribonuclease P: an enzyme with an essential RNA component

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16S ribosomal RNA.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788923

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

26 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP576

Crystal structure of yeast phenylalanine transfer RNA

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP576

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19812110

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTP576

1 reference

journals/bioinformatics/JonikasRA09

20 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

20 August 2017

1 reference

PMCID

2788923