(Q35651055)

9 August 2017

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (English)

1 reference

9 August 2017

Rhiju Das

3

0 references

author name string

Parin Sripakdeevong

series ordinal

1

1 reference

PubMed ID

22143768

9 August 2017

Wipapat Kladwang

series ordinal

2

1 reference

PubMed ID

22143768

9 August 2017

language of work or name

English

0 references

publication date

5 December 2011

1 reference

Proceedings of the National Academy of Sciences of the United States of America

9 August 2017

1 reference

9 August 2017

108

1 reference

9 August 2017

51

1 reference

9 August 2017

20573-20578

1 reference

Four small puzzles that Rosetta doesn't solve

9 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Rosetta in CAPRI rounds 13-19.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Nuclear magnetic resonance structure of the prohead RNA E-loop hairpin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Atomic accuracy in predicting and designing noncanonical RNA structure

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Current status of the AMOEBA polarizable force field

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Sampling bottlenecks in de novo protein structure prediction

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Blind test of physics-based prediction of protein structures.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Consistent blind protein structure generation from NMR chemical shift data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Synthetic antibodies for specific recognition and crystallization of structured RNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

DMS footprinting of structured RNAs and RNA-protein complexes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Automated de novo prediction of native-like RNA tertiary structures

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Routes are trees: the parsing perspective on protein folding.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Computational redesign of endonuclease DNA binding and cleavage specificity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Prediction of novel and analogous folds using fragment assembly and fold recognition.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Protein structure prediction using Rosetta

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Geometric nomenclature and classification of RNA base pairs

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Modeling active RNA structures using the intersection of conformational space: application to the lead-activated ribozyme.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

A network of heterogeneous hydrogen bonds in GNRA tetraloops

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Comparative biosequence metrics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Turning limited experimental information into 3D models of RNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Critical assessment of methods of protein structure prediction - Round VIII.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Frequency and isostericity of RNA base pairs

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

High-resolution structure prediction and the crystallographic phase problem

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

A density-functional study on pi-aromatic interaction: benzene dimer and naphthalene dimer.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Toward high-resolution de novo structure prediction for small proteins.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Computational alanine scanning of protein-protein interfaces

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3251086

Interpeptide interactions induce helix to strand structural transition in Abeta peptides

25 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1106516108

RNA secondary structures and their prediction

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1106516108

Control of memory formation through regulated expression of a CaMKII transgene

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1106516108

21 January 2018

Identifiers

DOI

10.1073/PNAS.1106516108

1 reference

9 August 2017

0 references

1 reference

9 August 2017

1 reference

PubMed ID

22143768