(Q35783573)

10 August 2017

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints (English)

1 reference

10 August 2017

Matthew G Seetin

1

1 reference

PubMed ID

21509787

10 August 2017

David H Mathews

series ordinal

2

1 reference

10 August 2017

21 April 2011

1 reference

Journal of Computational Chemistry

10 August 2017

1 reference

10 August 2017

32

1 reference

10 August 2017

10

1 reference

10 August 2017

2232-2244

1 reference

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

On the significance of an RNA tertiary structure prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

LOOS: an extensible platform for the structural analysis of simulations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

iFoldRNA: three-dimensional RNA structure prediction and folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Automated de novo prediction of native-like RNA tertiary structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Predicting helical coaxial stacking in RNA multibranch loops

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Tertiary contacts distant from the active site prime a ribozyme for catalysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Rfam: an RNA family database

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Structure and assembly of the Alu domain of the mammalian signal recognition particle

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

MANIP: an interactive tool for modelling RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Compilation of tRNA sequences and sequences of tRNA genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

RNA tertiary structure mediation by adenosine platforms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Areas, volumes, packing and protein structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3288334

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

12 July 2018

1 reference

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

21 January 2018

1 reference

Photocrosslinking detects a compact, active structure of the hammerhead ribozyme

21 January 2018

1 reference

Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Pairwise solute descreening of solute charges from a dielectric medium

21 January 2018

1 reference

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

21 January 2018

1 reference

A Poisson–Boltzmann dynamics method with nonperiodic boundary condition

21 January 2018

1 reference

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21509787

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure of an unmodified tRNA molecule

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21509787

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/JCC.21806

1 reference

10 August 2017

journals/jcc/SeetinM11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

10 August 2017

1 reference

PubMed ID

21509787